Merge branch 'main' into err

cmd/invoke_tool_test.go

@@ -1,131 +0,0 @@
-// Copyright 2026 Google LLC
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//     http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
-
-package cmd
-
-import (
-	"context"
-	"os"
-	"path/filepath"
-	"strings"
-	"testing"
-)
-
-func TestInvokeTool(t *testing.T) {
-	// Create a temporary tools file
-	tmpDir := t.TempDir()
-
-	toolsFileContent := `
-sources:
-  my-sqlite:
-    kind: sqlite
-    database: test.db
-tools:
-  hello-sqlite:
-    kind: sqlite-sql
-    source: my-sqlite
-    description: "hello tool"
-    statement: "SELECT 'hello' as greeting"
-  echo-tool:
-    kind: sqlite-sql
-    source: my-sqlite
-    description: "echo tool"
-    statement: "SELECT ? as msg"
-    parameters:
-      - name: message
-        type: string
-        description: message to echo
-`
-
-	toolsFilePath := filepath.Join(tmpDir, "tools.yaml")
-	if err := os.WriteFile(toolsFilePath, []byte(toolsFileContent), 0644); err != nil {
-		t.Fatalf("failed to write tools file: %v", err)
-	}
-
-	tcs := []struct {
-		desc    string
-		args    []string
-		want    string
-		wantErr bool
-		errStr  string
-	}{
-		{
-			desc: "success - basic tool call",
-			args: []string{"invoke", "hello-sqlite", "--tools-file", toolsFilePath},
-			want: `"greeting": "hello"`,
-		},
-		{
-			desc: "success - tool call with parameters",
-			args: []string{"invoke", "echo-tool", `{"message": "world"}`, "--tools-file", toolsFilePath},
-			want: `"msg": "world"`,
-		},
-		{
-			desc:    "error - tool not found",
-			args:    []string{"invoke", "non-existent", "--tools-file", toolsFilePath},
-			wantErr: true,
-			errStr:  `tool "non-existent" not found`,
-		},
-		{
-			desc:    "error - invalid JSON params",
-			args:    []string{"invoke", "echo-tool", `invalid-json`, "--tools-file", toolsFilePath},
-			wantErr: true,
-			errStr:  `params must be a valid JSON string`,
-		},
-	}
-
-	for _, tc := range tcs {
-		t.Run(tc.desc, func(t *testing.T) {
-			_, got, err := invokeCommandWithContext(context.Background(), tc.args)
-			if (err != nil) != tc.wantErr {
-				t.Fatalf("got error %v, wantErr %v", err, tc.wantErr)
-			}
-			if tc.wantErr && !strings.Contains(err.Error(), tc.errStr) {
-				t.Fatalf("got error %v, want error containing %q", err, tc.errStr)
-			}
-			if !tc.wantErr && !strings.Contains(got, tc.want) {
-				t.Fatalf("got %q, want it to contain %q", got, tc.want)
-			}
-		})
-	}
-}
-
-func TestInvokeTool_AuthUnsupported(t *testing.T) {
-	tmpDir := t.TempDir()
-	toolsFileContent := `
-sources:
-  my-bq:
-    kind: bigquery
-    project: my-project
-    useClientOAuth: true
-tools:
-  bq-tool:
-    kind: bigquery-sql
-    source: my-bq
-    description: "bq tool"
-    statement: "SELECT 1"
-`
-	toolsFilePath := filepath.Join(tmpDir, "auth_tools.yaml")
-	if err := os.WriteFile(toolsFilePath, []byte(toolsFileContent), 0644); err != nil {
-		t.Fatalf("failed to write tools file: %v", err)
-	}
-
-	args := []string{"invoke", "bq-tool", "--tools-file", toolsFilePath}
-	_, _, err := invokeCommandWithContext(context.Background(), args)
-	if err == nil {
-		t.Fatal("expected error for tool requiring client auth, but got nil")
-	}
-	if !strings.Contains(err.Error(), "client authorization is not supported") {
-		t.Fatalf("unexpected error message: %v", err)
-	}
-}

cmd/root.go

@@ -34,8 +34,6 @@ import (
 	"github.com/fsnotify/fsnotify"
 	yaml "github.com/goccy/go-yaml"
 	"github.com/googleapis/genai-toolbox/internal/auth"
-	"github.com/googleapis/genai-toolbox/internal/cli/invoke"
-	"github.com/googleapis/genai-toolbox/internal/cli/skills"
 	"github.com/googleapis/genai-toolbox/internal/embeddingmodels"
 	"github.com/googleapis/genai-toolbox/internal/log"
 	"github.com/googleapis/genai-toolbox/internal/prebuiltconfigs"
@@ -367,44 +365,37 @@ func NewCommand(opts ...Option) *Command {
 	baseCmd.SetErr(cmd.errStream)
 
 	flags := cmd.Flags()
-	persistentFlags := cmd.PersistentFlags()
-
 	flags.StringVarP(&cmd.cfg.Address, "address", "a", "127.0.0.1", "Address of the interface the server will listen on.")
 	flags.IntVarP(&cmd.cfg.Port, "port", "p", 5000, "Port the server will listen on.")
 
 	flags.StringVar(&cmd.tools_file, "tools_file", "", "File path specifying the tool configuration. Cannot be used with --tools-files, or --tools-folder.")
 	// deprecate tools_file
 	_ = flags.MarkDeprecated("tools_file", "please use --tools-file instead")
-	persistentFlags.StringVar(&cmd.tools_file, "tools-file", "", "File path specifying the tool configuration. Cannot be used with --tools-files, or --tools-folder.")
+	flags.StringVar(&cmd.tools_file, "tools-file", "", "File path specifying the tool configuration. Cannot be used with --tools-files, or --tools-folder.")
-	persistentFlags.StringSliceVar(&cmd.tools_files, "tools-files", []string{}, "Multiple file paths specifying tool configurations. Files will be merged. Cannot be used with --tools-file, or --tools-folder.")
+	flags.StringSliceVar(&cmd.tools_files, "tools-files", []string{}, "Multiple file paths specifying tool configurations. Files will be merged. Cannot be used with --tools-file, or --tools-folder.")
-	persistentFlags.StringVar(&cmd.tools_folder, "tools-folder", "", "Directory path containing YAML tool configuration files. All .yaml and .yml files in the directory will be loaded and merged. Cannot be used with --tools-file, or --tools-files.")
+	flags.StringVar(&cmd.tools_folder, "tools-folder", "", "Directory path containing YAML tool configuration files. All .yaml and .yml files in the directory will be loaded and merged. Cannot be used with --tools-file, or --tools-files.")
-	persistentFlags.Var(&cmd.cfg.LogLevel, "log-level", "Specify the minimum level logged. Allowed: 'DEBUG', 'INFO', 'WARN', 'ERROR'.")
+	flags.Var(&cmd.cfg.LogLevel, "log-level", "Specify the minimum level logged. Allowed: 'DEBUG', 'INFO', 'WARN', 'ERROR'.")
-	persistentFlags.Var(&cmd.cfg.LoggingFormat, "logging-format", "Specify logging format to use. Allowed: 'standard' or 'JSON'.")
+	flags.Var(&cmd.cfg.LoggingFormat, "logging-format", "Specify logging format to use. Allowed: 'standard' or 'JSON'.")
-	persistentFlags.BoolVar(&cmd.cfg.TelemetryGCP, "telemetry-gcp", false, "Enable exporting directly to Google Cloud Monitoring.")
+	flags.BoolVar(&cmd.cfg.TelemetryGCP, "telemetry-gcp", false, "Enable exporting directly to Google Cloud Monitoring.")
-	persistentFlags.StringVar(&cmd.cfg.TelemetryOTLP, "telemetry-otlp", "", "Enable exporting using OpenTelemetry Protocol (OTLP) to the specified endpoint (e.g. 'http://127.0.0.1:4318')")
+	flags.StringVar(&cmd.cfg.TelemetryOTLP, "telemetry-otlp", "", "Enable exporting using OpenTelemetry Protocol (OTLP) to the specified endpoint (e.g. 'http://127.0.0.1:4318')")
-	persistentFlags.StringVar(&cmd.cfg.TelemetryServiceName, "telemetry-service-name", "toolbox", "Sets the value of the service.name resource attribute for telemetry data.")
+	flags.StringVar(&cmd.cfg.TelemetryServiceName, "telemetry-service-name", "toolbox", "Sets the value of the service.name resource attribute for telemetry data.")
 	// Fetch prebuilt tools sources to customize the help description
 	prebuiltHelp := fmt.Sprintf(
 		"Use a prebuilt tool configuration by source type. Allowed: '%s'. Can be specified multiple times.",
 		strings.Join(prebuiltconfigs.GetPrebuiltSources(), "', '"),
 	)
-	persistentFlags.StringSliceVar(&cmd.prebuiltConfigs, "prebuilt", []string{}, prebuiltHelp)
+	flags.StringSliceVar(&cmd.prebuiltConfigs, "prebuilt", []string{}, prebuiltHelp)
 	flags.BoolVar(&cmd.cfg.Stdio, "stdio", false, "Listens via MCP STDIO instead of acting as a remote HTTP server.")
 	flags.BoolVar(&cmd.cfg.DisableReload, "disable-reload", false, "Disables dynamic reloading of tools file.")
 	flags.BoolVar(&cmd.cfg.UI, "ui", false, "Launches the Toolbox UI web server.")
 	// TODO: Insecure by default. Might consider updating this for v1.0.0
 	flags.StringSliceVar(&cmd.cfg.AllowedOrigins, "allowed-origins", []string{"*"}, "Specifies a list of origins permitted to access this server. Defaults to '*'.")
 	flags.StringSliceVar(&cmd.cfg.AllowedHosts, "allowed-hosts", []string{"*"}, "Specifies a list of hosts permitted to access this server. Defaults to '*'.")
-	persistentFlags.StringSliceVar(&cmd.cfg.UserAgentMetadata, "user-agent-metadata", []string{}, "Appends additional metadata to the User-Agent.")
+	flags.StringSliceVar(&cmd.cfg.UserAgentMetadata, "user-agent-metadata", []string{}, "Appends additional metadata to the User-Agent.")
 
 	// wrap RunE command so that we have access to original Command object
 	cmd.RunE = func(*cobra.Command, []string) error { return run(cmd) }
 
-	// Register subcommands for tool invocation
-	baseCmd.AddCommand(invoke.NewCommand(cmd))
-	// Register subcommands for skill generation
-	baseCmd.AddCommand(skills.NewCommand(cmd))
-
 	return cmd
 }
 
@@ -928,24 +919,71 @@ func resolveWatcherInputs(toolsFile string, toolsFiles []string, toolsFolder str
 	return watchDirs, watchedFiles
 }
 
-func (cmd *Command) Config() server.ServerConfig {
+func run(cmd *Command) error {
-	return cmd.cfg
+	ctx, cancel := context.WithCancel(cmd.Context())
-}
+	defer cancel()
 
-func (cmd *Command) Out() io.Writer {
+	// watch for sigterm / sigint signals
-	return cmd.outStream
+	signals := make(chan os.Signal, 1)
-}
+	signal.Notify(signals, syscall.SIGTERM, syscall.SIGINT)
+	go func(sCtx context.Context) {
+		var s os.Signal
+		select {
+		case <-sCtx.Done():
+			// this should only happen when the context supplied when testing is canceled
+			return
+		case s = <-signals:
+		}
+		switch s {
+		case syscall.SIGINT:
+			cmd.logger.DebugContext(sCtx, "Received SIGINT signal to shutdown.")
+		case syscall.SIGTERM:
+			cmd.logger.DebugContext(sCtx, "Sending SIGTERM signal to shutdown.")
+		}
+		cancel()
+	}(ctx)
 
-func (cmd *Command) Logger() log.Logger {
+	// If stdio, set logger's out stream (usually DEBUG and INFO logs) to errStream
-	return cmd.logger
+	loggerOut := cmd.outStream
-}
+	if cmd.cfg.Stdio {
-
+		loggerOut = cmd.errStream
-func (cmd *Command) LoadConfig(ctx context.Context) error {
-	logger, err := util.LoggerFromContext(ctx)
-	if err != nil {
-		return err
 	}
 
+	// Handle logger separately from config
+	switch strings.ToLower(cmd.cfg.LoggingFormat.String()) {
+	case "json":
+		logger, err := log.NewStructuredLogger(loggerOut, cmd.errStream, cmd.cfg.LogLevel.String())
+		if err != nil {
+			return fmt.Errorf("unable to initialize logger: %w", err)
+		}
+		cmd.logger = logger
+	case "standard":
+		logger, err := log.NewStdLogger(loggerOut, cmd.errStream, cmd.cfg.LogLevel.String())
+		if err != nil {
+			return fmt.Errorf("unable to initialize logger: %w", err)
+		}
+		cmd.logger = logger
+	default:
+		return fmt.Errorf("logging format invalid")
+	}
+
+	ctx = util.WithLogger(ctx, cmd.logger)
+
+	// Set up OpenTelemetry
+	otelShutdown, err := telemetry.SetupOTel(ctx, cmd.cfg.Version, cmd.cfg.TelemetryOTLP, cmd.cfg.TelemetryGCP, cmd.cfg.TelemetryServiceName)
+	if err != nil {
+		errMsg := fmt.Errorf("error setting up OpenTelemetry: %w", err)
+		cmd.logger.ErrorContext(ctx, errMsg.Error())
+		return errMsg
+	}
+	defer func() {
+		err := otelShutdown(ctx)
+		if err != nil {
+			errMsg := fmt.Errorf("error shutting down OpenTelemetry: %w", err)
+			cmd.logger.ErrorContext(ctx, errMsg.Error())
+		}
+	}()
+
 	var allToolsFiles []ToolsFile
 
 	// Load Prebuilt Configuration
@@ -954,12 +992,12 @@ func (cmd *Command) LoadConfig(ctx context.Context) error {
 		slices.Sort(cmd.prebuiltConfigs)
 		sourcesList := strings.Join(cmd.prebuiltConfigs, ", ")
 		logMsg := fmt.Sprintf("Using prebuilt tool configurations for: %s", sourcesList)
-		logger.InfoContext(ctx, logMsg)
+		cmd.logger.InfoContext(ctx, logMsg)
 
 		for _, configName := range cmd.prebuiltConfigs {
 			buf, err := prebuiltconfigs.Get(configName)
 			if err != nil {
-				logger.ErrorContext(ctx, err.Error())
+				cmd.logger.ErrorContext(ctx, err.Error())
 				return err
 			}
 
@@ -967,7 +1005,7 @@ func (cmd *Command) LoadConfig(ctx context.Context) error {
 			parsed, err := parseToolsFile(ctx, buf)
 			if err != nil {
 				errMsg := fmt.Errorf("unable to parse prebuilt tool configuration for '%s': %w", configName, err)
-				logger.ErrorContext(ctx, errMsg.Error())
+				cmd.logger.ErrorContext(ctx, errMsg.Error())
 				return errMsg
 			}
 			allToolsFiles = append(allToolsFiles, parsed)
@@ -993,7 +1031,7 @@ func (cmd *Command) LoadConfig(ctx context.Context) error {
 			(cmd.tools_file != "" && cmd.tools_folder != "") ||
 			(len(cmd.tools_files) > 0 && cmd.tools_folder != "") {
 			errMsg := fmt.Errorf("--tools-file, --tools-files, and --tools-folder flags cannot be used simultaneously")
-			logger.ErrorContext(ctx, errMsg.Error())
+			cmd.logger.ErrorContext(ctx, errMsg.Error())
 			return errMsg
 		}
 
@@ -1002,18 +1040,18 @@ func (cmd *Command) LoadConfig(ctx context.Context) error {
 
 		if len(cmd.tools_files) > 0 {
 			// Use tools-files
-			logger.InfoContext(ctx, fmt.Sprintf("Loading and merging %d tool configuration files", len(cmd.tools_files)))
+			cmd.logger.InfoContext(ctx, fmt.Sprintf("Loading and merging %d tool configuration files", len(cmd.tools_files)))
 			customTools, err = loadAndMergeToolsFiles(ctx, cmd.tools_files)
 		} else if cmd.tools_folder != "" {
 			// Use tools-folder
-			logger.InfoContext(ctx, fmt.Sprintf("Loading and merging all YAML files from directory: %s", cmd.tools_folder))
+			cmd.logger.InfoContext(ctx, fmt.Sprintf("Loading and merging all YAML files from directory: %s", cmd.tools_folder))
 			customTools, err = loadAndMergeToolsFolder(ctx, cmd.tools_folder)
 		} else {
 			// Use single file (tools-file or default `tools.yaml`)
 			buf, readFileErr := os.ReadFile(cmd.tools_file)
 			if readFileErr != nil {
 				errMsg := fmt.Errorf("unable to read tool file at %q: %w", cmd.tools_file, readFileErr)
-				logger.ErrorContext(ctx, errMsg.Error())
+				cmd.logger.ErrorContext(ctx, errMsg.Error())
 				return errMsg
 			}
 			customTools, err = parseToolsFile(ctx, buf)
@@ -1023,7 +1061,7 @@ func (cmd *Command) LoadConfig(ctx context.Context) error {
 		}
 
 		if err != nil {
-			logger.ErrorContext(ctx, err.Error())
+			cmd.logger.ErrorContext(ctx, err.Error())
 			return err
 		}
 		allToolsFiles = append(allToolsFiles, customTools)
@@ -1045,7 +1083,7 @@ func (cmd *Command) LoadConfig(ctx context.Context) error {
 	// This will error if custom tools collide with prebuilt tools
 	finalToolsFile, err := mergeToolsFiles(allToolsFiles...)
 	if err != nil {
-		logger.ErrorContext(ctx, err.Error())
+		cmd.logger.ErrorContext(ctx, err.Error())
 		return err
 	}
 
@@ -1056,91 +1094,15 @@ func (cmd *Command) LoadConfig(ctx context.Context) error {
 	cmd.cfg.ToolsetConfigs = finalToolsFile.Toolsets
 	cmd.cfg.PromptConfigs = finalToolsFile.Prompts
 
-	return nil
+	instrumentation, err := telemetry.CreateTelemetryInstrumentation(versionString)
-}
-
-func (cmd *Command) Setup(ctx context.Context) (context.Context, func(context.Context) error, error) {
-	// If stdio, set logger's out stream (usually DEBUG and INFO logs) to errStream
-	loggerOut := cmd.outStream
-	if cmd.cfg.Stdio {
-		loggerOut = cmd.errStream
-	}
-
-	// Handle logger separately from config
-	logger, err := log.NewLogger(cmd.cfg.LoggingFormat.String(), cmd.cfg.LogLevel.String(), loggerOut, cmd.errStream)
-	if err != nil {
-		return ctx, nil, fmt.Errorf("unable to initialize logger: %w", err)
-	}
-	cmd.logger = logger
-
-	ctx = util.WithLogger(ctx, cmd.logger)
-
-	// Set up OpenTelemetry
-	otelShutdown, err := telemetry.SetupOTel(ctx, cmd.cfg.Version, cmd.cfg.TelemetryOTLP, cmd.cfg.TelemetryGCP, cmd.cfg.TelemetryServiceName)
-	if err != nil {
-		errMsg := fmt.Errorf("error setting up OpenTelemetry: %w", err)
-		cmd.logger.ErrorContext(ctx, errMsg.Error())
-		return ctx, nil, errMsg
-	}
-
-	shutdownFunc := func(ctx context.Context) error {
-		err := otelShutdown(ctx)
-		if err != nil {
-			errMsg := fmt.Errorf("error shutting down OpenTelemetry: %w", err)
-			cmd.logger.ErrorContext(ctx, errMsg.Error())
-			return err
-		}
-		return nil
-	}
-
-	instrumentation, err := telemetry.CreateTelemetryInstrumentation(cmd.cfg.Version)
 	if err != nil {
 		errMsg := fmt.Errorf("unable to create telemetry instrumentation: %w", err)
 		cmd.logger.ErrorContext(ctx, errMsg.Error())
-		return ctx, shutdownFunc, errMsg
+		return errMsg
 	}
 
 	ctx = util.WithInstrumentation(ctx, instrumentation)
 
-	return ctx, shutdownFunc, nil
-}
-
-func run(cmd *Command) error {
-	ctx, cancel := context.WithCancel(cmd.Context())
-	defer cancel()
-
-	// watch for sigterm / sigint signals
-	signals := make(chan os.Signal, 1)
-	signal.Notify(signals, syscall.SIGTERM, syscall.SIGINT)
-	go func(sCtx context.Context) {
-		var s os.Signal
-		select {
-		case <-sCtx.Done():
-			// this should only happen when the context supplied when testing is canceled
-			return
-		case s = <-signals:
-		}
-		switch s {
-		case syscall.SIGINT:
-			cmd.logger.DebugContext(sCtx, "Received SIGINT signal to shutdown.")
-		case syscall.SIGTERM:
-			cmd.logger.DebugContext(sCtx, "Sending SIGTERM signal to shutdown.")
-		}
-		cancel()
-	}(ctx)
-
-	ctx, shutdown, err := cmd.Setup(ctx)
-	if err != nil {
-		return err
-	}
-	defer func() {
-		_ = shutdown(ctx)
-	}()
-
-	if err := cmd.LoadConfig(ctx); err != nil {
-		return err
-	}
-
 	// start server
 	s, err := server.NewServer(ctx, cmd.cfg)
 	if err != nil {
@@ -1180,9 +1142,6 @@ func run(cmd *Command) error {
 		}()
 	}
 
-	// Determine if Custom Files are configured (re-check as loadAndMergeConfig might have updated defaults)
-	isCustomConfigured := cmd.tools_file != "" || len(cmd.tools_files) > 0 || cmd.tools_folder != ""
-
 	if isCustomConfigured && !cmd.cfg.DisableReload {
 		watchDirs, watchedFiles := resolveWatcherInputs(cmd.tools_file, cmd.tools_files, cmd.tools_folder)
 		// start watching the file(s) or folder for changes to trigger dynamic reloading

cmd/skill_generate_test.go

@@ -1,166 +0,0 @@
-// Copyright 2026 Google LLC
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//     http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
-
-package cmd
-
-import (
-	"context"
-	"os"
-	"path/filepath"
-	"strings"
-	"testing"
-	"time"
-)
-
-func TestGenerateSkill(t *testing.T) {
-	// Create a temporary directory for tests
-	tmpDir := t.TempDir()
-	outputDir := filepath.Join(tmpDir, "skills")
-
-	// Create a tools.yaml file with a sqlite tool
-	toolsFileContent := `
-sources:
-  my-sqlite:
-    kind: sqlite
-    database: test.db
-tools:
-  hello-sqlite:
-    kind: sqlite-sql
-    source: my-sqlite
-    description: "hello tool"
-    statement: "SELECT 'hello' as greeting"
-`
-
-	toolsFilePath := filepath.Join(tmpDir, "tools.yaml")
-	if err := os.WriteFile(toolsFilePath, []byte(toolsFileContent), 0644); err != nil {
-		t.Fatalf("failed to write tools file: %v", err)
-	}
-
-	args := []string{
-		"skills-generate",
-		"--tools-file", toolsFilePath,
-		"--output-dir", outputDir,
-		"--name", "hello-sqlite",
-		"--description", "hello tool",
-	}
-
-	// We need a longer timeout because generate-skill starts a server and polls it
-	ctx, cancel := context.WithTimeout(context.Background(), 30*time.Second)
-	defer cancel()
-
-	_, got, err := invokeCommandWithContext(ctx, args)
-	if err != nil {
-		t.Fatalf("command failed: %v\nOutput: %s", err, got)
-	}
-
-	// Verify generated directory structure
-	skillPath := filepath.Join(outputDir, "hello-sqlite")
-	if _, err := os.Stat(skillPath); os.IsNotExist(err) {
-		t.Fatalf("skill directory not created: %s", skillPath)
-	}
-
-	// Check SKILL.md
-	skillMarkdown := filepath.Join(skillPath, "SKILL.md")
-	content, err := os.ReadFile(skillMarkdown)
-	if err != nil {
-		t.Fatalf("failed to read SKILL.md: %v", err)
-	}
-	if !strings.Contains(string(content), "name: hello-sqlite") {
-		t.Errorf("SKILL.md does not contain expected name")
-	}
-	if !strings.Contains(string(content), "description: hello tool") {
-		t.Errorf("SKILL.md does not contain expected description")
-	}
-
-	// Check script file
-	scriptFilename := "hello-sqlite.js"
-	scriptPath := filepath.Join(skillPath, "scripts", scriptFilename)
-	if _, err := os.Stat(scriptPath); os.IsNotExist(err) {
-		t.Fatalf("script file not created: %s", scriptPath)
-	}
-
-	scriptContent, err := os.ReadFile(scriptPath)
-	if err != nil {
-		t.Fatalf("failed to read script file: %v", err)
-	}
-	if !strings.Contains(string(scriptContent), "hello-sqlite") {
-		t.Errorf("script file does not contain expected tool name")
-	}
-
-	// Check assets
-	assetPath := filepath.Join(skillPath, "assets", "hello-sqlite.yaml")
-	if _, err := os.Stat(assetPath); os.IsNotExist(err) {
-		t.Fatalf("asset file not created: %s", assetPath)
-	}
-	assetContent, err := os.ReadFile(assetPath)
-	if err != nil {
-		t.Fatalf("failed to read asset file: %v", err)
-	}
-	if !strings.Contains(string(assetContent), "hello-sqlite") {
-		t.Errorf("asset file does not contain expected tool name")
-	}
-}
-
-func TestGenerateSkill_NoConfig(t *testing.T) {
-	tmpDir := t.TempDir()
-	outputDir := filepath.Join(tmpDir, "skills")
-
-	args := []string{
-		"skills-generate",
-		"--output-dir", outputDir,
-		"--name", "test",
-		"--description", "test",
-	}
-
-	_, _, err := invokeCommandWithContext(context.Background(), args)
-	if err == nil {
-		t.Fatal("expected command to fail when no configuration is provided and tools.yaml is missing")
-	}
-
-	// Should not have created the directory if no config was processed
-	if _, err := os.Stat(outputDir); !os.IsNotExist(err) {
-		t.Errorf("output directory should not have been created")
-	}
-}
-
-func TestGenerateSkill_MissingArguments(t *testing.T) {
-	tmpDir := t.TempDir()
-	toolsFilePath := filepath.Join(tmpDir, "tools.yaml")
-	if err := os.WriteFile(toolsFilePath, []byte("tools: {}"), 0644); err != nil {
-		t.Fatalf("failed to write tools file: %v", err)
-	}
-
-	tests := []struct {
-		name string
-		args []string
-	}{
-		{
-			name: "missing name",
-			args: []string{"skills-generate", "--tools-file", toolsFilePath, "--description", "test"},
-		},
-		{
-			name: "missing description",
-			args: []string{"skills-generate", "--tools-file", toolsFilePath, "--name", "test"},
-		},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			_, got, err := invokeCommandWithContext(context.Background(), tt.args)
-			if err == nil {
-				t.Fatalf("expected command to fail due to missing arguments, but it succeeded\nOutput: %s", got)
-			}
-		})
-	}
-}

docs/en/how-to/generate_skill.md

@@ -1,107 +0,0 @@
----
-title: "Generate a Skill"
-type: docs
-weight: 10
-description: >
-  How to generate a skill from a toolset configuration.
----
-
-The `skills-generate` command allows you to convert a **toolset** into a **skill**. A toolset is a collection of tools, and the generated skill will contain metadata and execution scripts for all tools within that toolset.
-
-## Before you begin
-
-1. Make sure you have the `toolbox` executable in your PATH.
-2. Make sure you have [Node.js](https://nodejs.org/) installed on your system.
-
-## Generating a Skill from a Toolset
-
-A skill package consists of a `SKILL.md` file and a set of Node.js scripts. Each tool defined in your toolset maps to a corresponding script in the generated skill.
-
-### Command Signature
-
-The `skills-generate` command follows this signature:
-
-```bash
-toolbox [--tools-file <path> | --prebuilt <name>] skills-generate \
-  --name <skill-name> \
-  --toolset <toolset-name> \
-  --description <description> \
-  --output-dir <output-directory>
-```
-
-### Example: Custom Tools File
-
-1. Create a `tools.yaml` file with a toolset and some tools:
-
-   ```yaml
-   tools:
-     tool_a:
-       description: "First tool"
-       run:
-         command: "echo 'Tool A'"
-     tool_b:
-       description: "Second tool"
-       run:
-         command: "echo 'Tool B'"
-   toolsets:
-     my_toolset:
-       tools:
-         - tool_a
-         - tool_b
-   ```
-
-2. Generate the skill:
-
-   ```bash
-   toolbox --tools-file tools.yaml skills-generate \
-     --name "my-multi-tool-skill" \
-     --toolset "my_toolset" \
-     --description "A skill containing multiple tools" \
-     --output-dir "generated-skills"
-   ```
-
-3. The generated skill directory structure:
-
-   ```text
-   generated-skills/
-   └── my-multi-tool-skill/
-       ├── SKILL.md
-       ├── assets/
-       │   ├── tool_a.yaml
-       │   └── tool_b.yaml
-       └── scripts/
-           ├── tool_a.js
-           └── tool_b.js
-   ```
-
-   In this example, the skill contains two Node.js scripts (`tool_a.js` and `tool_b.js`), each mapping to a tool in the original toolset.
-
-### Example: Prebuilt Configuration
-
-You can also generate skills from prebuilt toolsets:
-
-```bash
-toolbox --prebuilt alloydb-postgres-admin skills-generate \
-  --name "alloydb-postgres-admin" \
-  --description "skill for performing administrative operations on alloydb"
-```
-
-## Output Directory
-
-By default, skills are generated in the `skills` directory. You can specify a different output directory using the `--output-dir` flag.
-
-## Shared Node.js Scripts
-
-The `skills-generate` command generates shared Node.js scripts (`.js`) that work across different platforms (Linux, macOS, Windows). This ensures that the generated skills are portable.
-
-## Installing the Generated Skill in Gemini CLI
-
-Once you have generated a skill, you can install it into the Gemini CLI using the `gemini skills install` command.
-
-### Installation Command
-
-Provide the path to the directory containing the generated skill:
-
-```bash
-gemini skills install /path/to/generated-skills/my-multi-tool-skill
-```

docs/en/how-to/invoke_tool.md

@@ -1,74 +0,0 @@
----
-title: "Invoke Tools via CLI"
-type: docs
-weight: 10
-description: >
-  Learn how to invoke your tools directly from the command line using the `invoke` command.
----
-
-The `invoke` command allows you to invoke tools defined in your configuration directly from the CLI. This is useful for:
-
-- **Ephemeral Invocation:** Executing a tool without spinning up a full MCP server/client.
-- **Debugging:** Isolating tool execution logic and testing with various parameter combinations.
-
-{{< notice tip >}}
-**Keep configurations minimal:** The `invoke` command initializes *all* resources (sources, tools, etc.) defined in your configuration files during execution. To ensure fast response times, consider using a minimal configuration file containing only the tools you need for the specific invocation.
-{{< notice tip >}}
-
-## Prerequisites
-
-- You have the `toolbox` binary installed or built.
-- You have a valid tool configuration file (e.g., `tools.yaml`).
-
-## Basic Usage
-
-The basic syntax for the command is:
-
-```bash
-toolbox [--tools-file <path> | --prebuilt <name>] invoke <tool-name> [params]
-```
-
-- `<tool-name>`: The name of the tool you want to call. This must match the name defined in your `tools.yaml`.
-- `[params]`: (Optional) A JSON string representing the arguments for the tool.
-
-## Examples
-
-### 1. Calling a Tool without Parameters
-
-If your tool takes no parameters, simply provide the tool name:
-
-```bash
-toolbox  --tools-file tools.yaml invoke my-simple-tool
-```
-
-### 2. Calling a Tool with Parameters
-
-For tools that require arguments, pass them as a JSON string. Ensure you escape quotes correctly for your shell.
-
-**Example: A tool that takes parameters**
-
-Assuming a tool named `mytool` taking `a` and `b`:
-
-```bash
-toolbox --tools-file tools.yaml invoke mytool '{"a": 10, "b": 20}' 
-```
-
-**Example: A tool that queries a database**
-
-```bash
-toolbox  --tools-file tools.yaml invoke db-query '{"sql": "SELECT * FROM users LIMIT 5"}'
-```
-
-### 3. Using Prebuilt Configurations
-
-You can also use the `--prebuilt` flag to load prebuilt toolsets.
-
-```bash
-toolbox --prebuilt cloudsql-postgres invoke cloudsql-postgres-list-instances
-```
-
-## Troubleshooting
-
-- **Tool not found:** Ensure the `<tool-name>` matches exactly what is in your YAML file and that the file is correctly loaded via `--tools-file`.
-- **Invalid parameters:** Double-check your JSON syntax. The error message will usually indicate if the JSON parsing failed or if the parameters didn't match the tool's schema.
-- **Auth errors:** The `invoke` command currently does not support flows requiring client-side authorization (like OAuth flow initiation via the CLI). It works best for tools using service-side authentication (e.g., Application Default Credentials).

docs/en/reference/cli.md

@@ -30,46 +30,6 @@ description: >
 |              | `--user-agent-metadata`    | Appends additional metadata to the User-Agent.                                                                                                                                   |             |
 | `-v`         | `--version`                | version for toolbox                                                                                                                                                              |             |
 
-## Sub Commands
-
-<details>
-<summary><code>invoke</code></summary>
-
-Executes a tool directly with the provided parameters. This is useful for testing tool configurations and parameters without needing a full client setup.
-
-**Syntax:**
-
-```bash
-toolbox invoke <tool-name> [params]
-```
-
-- `<tool-name>`: The name of the tool to execute (as defined in your configuration).
-- `[params]`: (Optional) A JSON string containing the parameters for the tool.
-
-</details>
-
-<details>
-<summary><code>skills-generate</code></summary>
-
-Generates a skill package from a specified toolset. Each tool in the toolset will have a corresponding Node.js execution script in the generated skill.
-
-**Syntax:**
-
-```bash
-toolbox [--tools-file <path> | --prebuilt <name>] skills-generate --name <name> --toolset <toolset> --description <description> --output-dir <output>
-```
-
-**Flags:**
-
-- `--name`: (Required) Name of the generated skill.
-- `--toolset`: (Required) Name of the toolset to convert into a skill.
-- `--description`: (Required) Description of the generated skill.
-- `--output-dir`: Directory to output generated skills (default: "skills").
-
-For more detailed instructions, see [Generate a Skill](../how-to/generate_skill.md).
-
-</details>
-
 ## Examples
 
 ### Transport Configuration

go.mod

@@ -52,7 +52,7 @@ require (
 	github.com/trinodb/trino-go-client v0.330.0
 	github.com/valkey-io/valkey-go v1.0.68
 	github.com/yugabyte/pgx/v5 v5.5.3-yb-5
-	go.mongodb.org/mongo-driver/v2 v2.4.2
+	go.mongodb.org/mongo-driver v1.17.4
 	go.opentelemetry.io/contrib/propagators/autoprop v0.62.0
 	go.opentelemetry.io/otel v1.38.0
 	go.opentelemetry.io/otel/exporters/otlp/otlpmetric/otlpmetrichttp v1.38.0
@@ -211,6 +211,7 @@ require (
 	github.com/moby/term v0.5.2 // indirect
 	github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd // indirect
 	github.com/modern-go/reflect2 v1.0.2 // indirect
+	github.com/montanaflynn/stats v0.7.1 // indirect
 	github.com/morikuni/aec v1.0.0 // indirect
 	github.com/mtibben/percent v0.2.1 // indirect
 	github.com/nakagami/chacha20 v0.1.0 // indirect

go.sum

@@ -1238,6 +1238,8 @@ github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd/go.mod h1:6dJ
 github.com/modern-go/reflect2 v1.0.2 h1:xBagoLtFs94CBntxluKeaWgTMpvLxC4ur3nMaC9Gz0M=
 github.com/modern-go/reflect2 v1.0.2/go.mod h1:yWuevngMOJpCy52FWWMvUC8ws7m/LJsjYzDa0/r8luk=
 github.com/montanaflynn/stats v0.0.0-20171201202039-1bf9dbcd8cbe/go.mod h1:wL8QJuTMNUDYhXwkmfOly8iTdp5TEcJFWZD2D7SIkUc=
+github.com/montanaflynn/stats v0.7.1 h1:etflOAAHORrCC44V+aR6Ftzort912ZU+YLiSTuV8eaE=
+github.com/montanaflynn/stats v0.7.1/go.mod h1:etXPPgVO6n31NxCd9KQUMvCM+ve0ruNzt6R8Bnaayow=
 github.com/morikuni/aec v1.0.0 h1:nP9CBfwrvYnBRgY6qfDQkygYDmYwOilePFkwzv4dU8A=
 github.com/morikuni/aec v1.0.0/go.mod h1:BbKIizmSmc5MMPqRYbxO4ZU0S0+P200+tUnFx7PXmsc=
 github.com/mtibben/percent v0.2.1 h1:5gssi8Nqo8QU/r2pynCm+hBQHpkB/uNK7BJCFogWdzs=
@@ -1402,8 +1404,8 @@ github.com/zeebo/xxh3 v1.0.2/go.mod h1:5NWz9Sef7zIDm2JHfFlcQvNekmcEl9ekUZQQKCYaD
 gitlab.com/nyarla/go-crypt v0.0.0-20160106005555-d9a5dc2b789b h1:7gd+rd8P3bqcn/96gOZa3F5dpJr/vEiDQYlNb/y2uNs=
 gitlab.com/nyarla/go-crypt v0.0.0-20160106005555-d9a5dc2b789b/go.mod h1:T3BPAOm2cqquPa0MKWeNkmOM5RQsRhkrwMWonFMN7fE=
 go.mongodb.org/mongo-driver v1.11.4/go.mod h1:PTSz5yu21bkT/wXpkS7WR5f0ddqw5quethTUn9WM+2g=
-go.mongodb.org/mongo-driver/v2 v2.4.2 h1:HrJ+Auygxceby9MLp3YITobef5a8Bv4HcPFIkml1U7U=
+go.mongodb.org/mongo-driver v1.17.4 h1:jUorfmVzljjr0FLzYQsGP8cgN/qzzxlY9Vh0C9KFXVw=
-go.mongodb.org/mongo-driver/v2 v2.4.2/go.mod h1:jHeEDJHJq7tm6ZF45Issun9dbogjfnPySb1vXA7EeAI=
+go.mongodb.org/mongo-driver v1.17.4/go.mod h1:Hy04i7O2kC4RS06ZrhPRqj/u4DTYkFDAAccj+rVKqgQ=
 go.opencensus.io v0.21.0/go.mod h1:mSImk1erAIZhrmZN+AvHh14ztQfjbGwt4TtuofqLduU=
 go.opencensus.io v0.22.0/go.mod h1:+kGneAE2xo2IficOXnaByMWTGM9T73dGwxeWcUqIpI8=
 go.opencensus.io v0.22.2/go.mod h1:yxeiOL68Rb0Xd1ddK5vPZ/oVn4vY4Ynel7k9FzqtOIw=

internal/cli/invoke/command.go

@@ -1,161 +0,0 @@
-// Copyright 2026 Google LLC
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//     http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
-
-package invoke
-
-import (
-	"context"
-	"encoding/json"
-	"fmt"
-	"io"
-
-	"github.com/googleapis/genai-toolbox/internal/log"
-	"github.com/googleapis/genai-toolbox/internal/server"
-	"github.com/googleapis/genai-toolbox/internal/server/resources"
-	"github.com/googleapis/genai-toolbox/internal/util/parameters"
-	"github.com/spf13/cobra"
-)
-
-// RootCommand defines the interface for required by invoke subcommand.
-// This allows subcommands to access shared resources and functionality without
-// direct coupling to the root command's implementation.
-type RootCommand interface {
-	// Config returns a copy of the current server configuration.
-	Config() server.ServerConfig
-
-	// Out returns the writer used for standard output.
-	Out() io.Writer
-
-	// LoadConfig loads and merges the configuration from files, folders, and prebuilts.
-	LoadConfig(ctx context.Context) error
-
-	// Setup initializes the runtime environment, including logging and telemetry.
-	// It returns the updated context and a shutdown function to be called when finished.
-	Setup(ctx context.Context) (context.Context, func(context.Context) error, error)
-
-	// Logger returns the logger instance.
-	Logger() log.Logger
-}
-
-func NewCommand(rootCmd RootCommand) *cobra.Command {
-	cmd := &cobra.Command{
-		Use:   "invoke <tool-name> [params]",
-		Short: "Execute a tool directly",
-		Long: `Execute a tool directly with parameters.
-Params must be a JSON string.
-Example:
-  toolbox invoke my-tool '{"param1": "value1"}'`,
-		Args: cobra.MinimumNArgs(1),
-		RunE: func(c *cobra.Command, args []string) error {
-			return runInvoke(c, args, rootCmd)
-		},
-	}
-	return cmd
-}
-
-func runInvoke(cmd *cobra.Command, args []string, rootCmd RootCommand) error {
-	ctx, cancel := context.WithCancel(cmd.Context())
-	defer cancel()
-
-	ctx, shutdown, err := rootCmd.Setup(ctx)
-	if err != nil {
-		return err
-	}
-	defer func() {
-		_ = shutdown(ctx)
-	}()
-
-	// Load and merge tool configurations
-	if err := rootCmd.LoadConfig(ctx); err != nil {
-		return err
-	}
-
-	// Initialize Resources
-	sourcesMap, authServicesMap, embeddingModelsMap, toolsMap, toolsetsMap, promptsMap, promptsetsMap, err := server.InitializeConfigs(ctx, rootCmd.Config())
-	if err != nil {
-		errMsg := fmt.Errorf("failed to initialize resources: %w", err)
-		rootCmd.Logger().ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	resourceMgr := resources.NewResourceManager(sourcesMap, authServicesMap, embeddingModelsMap, toolsMap, toolsetsMap, promptsMap, promptsetsMap)
-
-	// Execute Tool
-	toolName := args[0]
-	tool, ok := resourceMgr.GetTool(toolName)
-	if !ok {
-		errMsg := fmt.Errorf("tool %q not found", toolName)
-		rootCmd.Logger().ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	var paramsInput string
-	if len(args) > 1 {
-		paramsInput = args[1]
-	}
-
-	params := make(map[string]any)
-	if paramsInput != "" {
-		if err := json.Unmarshal([]byte(paramsInput), &params); err != nil {
-			errMsg := fmt.Errorf("params must be a valid JSON string: %w", err)
-			rootCmd.Logger().ErrorContext(ctx, errMsg.Error())
-			return errMsg
-		}
-	}
-
-	parsedParams, err := parameters.ParseParams(tool.GetParameters(), params, nil)
-	if err != nil {
-		errMsg := fmt.Errorf("invalid parameters: %w", err)
-		rootCmd.Logger().ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	parsedParams, err = tool.EmbedParams(ctx, parsedParams, resourceMgr.GetEmbeddingModelMap())
-	if err != nil {
-		errMsg := fmt.Errorf("error embedding parameters: %w", err)
-		rootCmd.Logger().ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	// Client Auth not supported for ephemeral CLI call
-	requiresAuth, err := tool.RequiresClientAuthorization(resourceMgr)
-	if err != nil {
-		errMsg := fmt.Errorf("failed to check auth requirements: %w", err)
-		rootCmd.Logger().ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-	if requiresAuth {
-		errMsg := fmt.Errorf("client authorization is not supported")
-		rootCmd.Logger().ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	result, err := tool.Invoke(ctx, resourceMgr, parsedParams, "")
-	if err != nil {
-		errMsg := fmt.Errorf("tool execution failed: %w", err)
-		rootCmd.Logger().ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	// Print Result
-	output, err := json.MarshalIndent(result, "", "  ")
-	if err != nil {
-		errMsg := fmt.Errorf("failed to marshal result: %w", err)
-		rootCmd.Logger().ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-	fmt.Fprintln(rootCmd.Out(), string(output))
-
-	return nil
-}

internal/cli/skills/command.go

@@ -1,298 +0,0 @@
-// Copyright 2026 Google LLC
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//     http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
-
-package skills
-
-import (
-	"context"
-	_ "embed"
-	"fmt"
-	"os"
-	"path/filepath"
-
-	"github.com/googleapis/genai-toolbox/internal/log"
-	"github.com/googleapis/genai-toolbox/internal/server"
-	"github.com/googleapis/genai-toolbox/internal/server/resources"
-
-	"github.com/spf13/cobra"
-)
-
-// RootCommand defines the interface for required by invoke subcommand.
-// This allows subcommands to access shared resources and functionality without
-// direct coupling to the root command's implementation.
-type RootCommand interface {
-	// Config returns a copy of the current server configuration.
-	Config() server.ServerConfig
-
-	// LoadConfig loads and merges the configuration from files, folders, and prebuilts.
-	LoadConfig(ctx context.Context) error
-
-	// Setup initializes the runtime environment, including logging and telemetry.
-	// It returns the updated context and a shutdown function to be called when finished.
-	Setup(ctx context.Context) (context.Context, func(context.Context) error, error)
-
-	// Logger returns the logger instance.
-	Logger() log.Logger
-}
-
-// Command is the command for generating skills.
-type Command struct {
-	*cobra.Command
-	rootCmd     RootCommand
-	name        string
-	description string
-	toolset     string
-	outputDir   string
-}
-
-// Parameter represents a parameter of a tool.
-type Parameter struct {
-	Name        string      `json:"name"`
-	Description string      `json:"description"`
-	Type        string      `json:"type"`
-	Default     interface{} `json:"default"`
-	Required    bool        `json:"required"`
-}
-
-// Tool represents a tool.
-type Tool struct {
-	Name        string      `json:"name"`
-	Description string      `json:"description"`
-	Parameters  []Parameter `json:"parameters"`
-}
-
-// Config represents the structure of the tools.yaml file.
-type Config struct {
-	Sources map[string]interface{}            `yaml:"sources,omitempty"`
-	Tools   map[string]map[string]interface{} `yaml:"tools"`
-}
-
-// serverConfig holds the configuration used to start the toolbox server.
-type serverConfig struct {
-	prebuiltConfigs []string
-	toolsFile       string
-}
-
-// NewCommand creates a new Command.
-func NewCommand(rootCmd RootCommand) *cobra.Command {
-	cmd := &Command{
-		rootCmd: rootCmd,
-	}
-	cmd.Command = &cobra.Command{
-		Use:   "skills-generate",
-		Short: "Generate skills from tool configurations",
-		RunE: func(c *cobra.Command, args []string) error {
-			return cmd.run(c)
-		},
-	}
-
-	cmd.Flags().StringVar(&cmd.outputDir, "output-dir", "skills", "Directory to output generated skills")
-	cmd.Flags().StringVar(&cmd.toolset, "toolset", "", "Name of the toolset (and generated skill folder). If provided, only tools in this toolset are generated.")
-	cmd.Flags().StringVar(&cmd.name, "name", "", "Name of the generated skill.")
-	cmd.Flags().StringVar(&cmd.description, "description", "", "Description of the generated skill")
-	cmd.MarkFlagRequired("name")
-	cmd.MarkFlagRequired("description")
-	return cmd.Command
-}
-
-func (c *Command) run(cmd *cobra.Command) error {
-	ctx, cancel := context.WithCancel(cmd.Context())
-	defer cancel()
-
-	ctx, shutdown, err := c.rootCmd.Setup(ctx)
-	if err != nil {
-		return err
-	}
-	defer func() {
-		_ = shutdown(ctx)
-	}()
-
-	logger := c.rootCmd.Logger()
-
-	toolsFile, err := cmd.Flags().GetString("tools-file")
-	if err != nil {
-		errMsg := fmt.Errorf("error getting tools-file flag: %w", err)
-		logger.ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-	prebuiltConfigs, err := cmd.Flags().GetStringSlice("prebuilt")
-	if err != nil {
-		errMsg := fmt.Errorf("error getting prebuilt flag: %w", err)
-		logger.ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	// Load and merge tool configurations
-	if err := c.rootCmd.LoadConfig(ctx); err != nil {
-		return err
-	}
-
-	if len(prebuiltConfigs) == 0 && toolsFile == "" {
-		logger.InfoContext(ctx, "No configurations found to process. Use --tools-file or --prebuilt.")
-		return nil
-	}
-	if err := os.MkdirAll(c.outputDir, 0755); err != nil {
-		errMsg := fmt.Errorf("error creating output directory: %w", err)
-		logger.ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	logger.InfoContext(ctx, fmt.Sprintf("Generating skill '%s'...", c.name))
-
-	config := serverConfig{
-		prebuiltConfigs: prebuiltConfigs,
-		toolsFile:       toolsFile,
-	}
-
-	// Initialize toolbox and collect tools
-	allTools, err := c.collectTools(ctx)
-	if err != nil {
-		errMsg := fmt.Errorf("error collecting tools: %w", err)
-		logger.ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	if len(allTools) == 0 {
-		logger.InfoContext(ctx, "No tools found to generate.")
-		return nil
-	}
-
-	// Generate the combined skill
-	skillPath := filepath.Join(c.outputDir, c.name)
-	if err := os.MkdirAll(skillPath, 0755); err != nil {
-		errMsg := fmt.Errorf("error creating skill directory: %w", err)
-		logger.ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	// Generate assets directory if needed
-	assetsPath := filepath.Join(skillPath, "assets")
-	if toolsFile != "" {
-		if err := os.MkdirAll(assetsPath, 0755); err != nil {
-			errMsg := fmt.Errorf("error creating assets dir: %w", err)
-			logger.ErrorContext(ctx, errMsg.Error())
-			return errMsg
-		}
-	}
-
-	// Generate scripts
-	scriptsPath := filepath.Join(skillPath, "scripts")
-	if err := os.MkdirAll(scriptsPath, 0755); err != nil {
-		errMsg := fmt.Errorf("error creating scripts dir: %w", err)
-		logger.ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	for _, tool := range allTools {
-		specificToolsFileName := ""
-		if toolsFile != "" {
-			minimizedContent, err := generateFilteredConfig(toolsFile, tool.Name)
-			if err != nil {
-				logger.ErrorContext(ctx, fmt.Sprintf("Error generating filtered config for %s: %v", tool.Name, err))
-			}
-
-			if minimizedContent != nil {
-				specificToolsFileName = fmt.Sprintf("%s.yaml", tool.Name)
-				destPath := filepath.Join(assetsPath, specificToolsFileName)
-				if err := os.WriteFile(destPath, minimizedContent, 0644); err != nil {
-					logger.ErrorContext(ctx, fmt.Sprintf("Error writing filtered config for %s: %v", tool.Name, err))
-				}
-			}
-		}
-
-		scriptContent, err := generateShellScriptContent(tool.Name, config, specificToolsFileName)
-		if err != nil {
-			logger.ErrorContext(ctx, fmt.Sprintf("Error generating script content for %s: %v", tool.Name, err))
-		} else {
-			scriptFilename := filepath.Join(scriptsPath, fmt.Sprintf("%s.js", tool.Name))
-			if err := os.WriteFile(scriptFilename, []byte(scriptContent), 0755); err != nil {
-				logger.ErrorContext(ctx, fmt.Sprintf("Error writing script %s: %v", scriptFilename, err))
-			}
-		}
-	}
-
-	// Generate SKILL.md
-	skillContent, err := generateSkillMarkdown(c.name, c.description, allTools)
-	if err != nil {
-		errMsg := fmt.Errorf("error generating SKILL.md content: %w", err)
-		logger.ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-	skillMdPath := filepath.Join(skillPath, "SKILL.md")
-	if err := os.WriteFile(skillMdPath, []byte(skillContent), 0644); err != nil {
-		errMsg := fmt.Errorf("error writing SKILL.md: %w", err)
-		logger.ErrorContext(ctx, errMsg.Error())
-		return errMsg
-	}
-
-	logger.InfoContext(ctx, fmt.Sprintf("Successfully generated skill '%s' with %d tools.", c.name, len(allTools)))
-
-	return nil
-}
-
-func (c *Command) collectTools(ctx context.Context) (map[string]Tool, error) {
-	// Initialize Resources
-	sourcesMap, authServicesMap, embeddingModelsMap, toolsMap, toolsetsMap, promptsMap, promptsetsMap, err := server.InitializeConfigs(ctx, c.rootCmd.Config())
-	if err != nil {
-		return nil, fmt.Errorf("failed to initialize resources: %w", err)
-	}
-
-	resourceMgr := resources.NewResourceManager(sourcesMap, authServicesMap, embeddingModelsMap, toolsMap, toolsetsMap, promptsMap, promptsetsMap)
-
-	result := make(map[string]Tool)
-
-	var toolsToProcess []string
-
-	if c.toolset != "" {
-		ts, ok := resourceMgr.GetToolset(c.toolset)
-		if !ok {
-			return nil, fmt.Errorf("toolset %q not found", c.toolset)
-		}
-		toolsToProcess = ts.ToolNames
-	} else {
-		// All tools
-		for name := range toolsMap {
-			toolsToProcess = append(toolsToProcess, name)
-		}
-	}
-
-	for _, toolName := range toolsToProcess {
-		t, ok := resourceMgr.GetTool(toolName)
-		if !ok {
-			// Should happen only if toolset refers to non-existent tool, but good to check
-			continue
-		}
-
-		params := []Parameter{}
-		for _, p := range t.GetParameters() {
-			manifest := p.Manifest()
-			params = append(params, Parameter{
-				Name:        p.GetName(),
-				Description: manifest.Description, // Use description from manifest
-				Type:        p.GetType(),
-				Default:     p.GetDefault(),
-				Required:    p.GetRequired(),
-			})
-		}
-
-		manifest := t.Manifest()
-		result[toolName] = Tool{
-			Name:        toolName,
-			Description: manifest.Description,
-			Parameters:  params,
-		}
-	}
-
-	return result, nil
-}

internal/cli/skills/generator.go

@@ -1,247 +0,0 @@
-// Copyright 2026 Google LLC
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//     http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
-
-package skills
-
-import (
-	"encoding/json"
-	"fmt"
-	"os"
-	"sort"
-	"strings"
-	"text/template"
-
-	"github.com/goccy/go-yaml"
-)
-
-const skillTemplate = `---
-name: {{.SkillName}}
-description: {{.SkillDescription}}
----
-
-Here is a list of scripts which can be used.
-
-{{range .Tools}}
-# {{.Name}}
-
-{{.Description}}
-
-{{.ParametersSchema}}
-
-## Usage
-
-{{.Usage}}
-
----
-{{end}}
-`
-
-type toolTemplateData struct {
-	Name             string
-	Description      string
-	ParametersSchema string
-	Usage            string
-}
-
-type skillTemplateData struct {
-	SkillName        string
-	SkillDescription string
-	Tools            []toolTemplateData
-}
-
-func generateSkillMarkdown(skillName, skillDescription string, toolsMap map[string]Tool) (string, error) {
-	var toolsData []toolTemplateData
-
-	// Order tools based on name
-	var tools []Tool
-	for _, tool := range toolsMap {
-		tools = append(tools, tool)
-	}
-	sort.Slice(tools, func(i, j int) bool {
-		return tools[i].Name < tools[j].Name
-	})
-
-	for _, tool := range tools {
-		parametersSchema, err := formatParameters(tool.Parameters)
-		if err != nil {
-			return "", err
-		}
-		usage := fmt.Sprintf("`bash\nnode scripts/%s.js '{\"<param_name>\": \"<param_value>\"}'\n`", tool.Name)
-
-		toolsData = append(toolsData, toolTemplateData{
-			Name:             tool.Name,
-			Description:      tool.Description,
-			ParametersSchema: parametersSchema,
-			Usage:            usage,
-		})
-	}
-
-	data := skillTemplateData{
-		SkillName:        skillName,
-		SkillDescription: skillDescription,
-		Tools:            toolsData,
-	}
-
-	tmpl, err := template.New("markdown").Parse(skillTemplate)
-	if err != nil {
-		return "", fmt.Errorf("error parsing markdown template: %w", err)
-	}
-
-	var buf strings.Builder
-	if err := tmpl.Execute(&buf, data); err != nil {
-		return "", fmt.Errorf("error executing markdown template: %w", err)
-	}
-
-	return buf.String(), nil
-}
-
-const nodeScriptTemplate = `#!/usr/bin/env node
-
-const { spawn } = require('child_process');
-const path = require('path');
-
-const toolName = "{{.Name}}";
-const prebuiltNames = {{.PrebuiltNamesJSON}};
-const toolsFileName = "{{.ToolsFileName}}";
-
-let configArgs = [];
-if (prebuiltNames.length > 0) {
-  prebuiltNames.forEach(name => {
-    configArgs.push("--prebuilt", name);
-  });
-}
-
-if (toolsFileName) {
-  configArgs.push("--tools-file", path.join(__dirname, "..", "assets", toolsFileName));
-}
-
-const args = process.argv.slice(2);
-const toolboxArgs = [...configArgs, "invoke", toolName, ...args];
-
-const command = process.platform === 'win32' ? 'toolbox.exe' : 'toolbox';
-
-const child = spawn(command, toolboxArgs, { stdio: 'inherit' });
-
-child.on('close', (code) => {
-  process.exit(code);
-});
-
-child.on('error', (err) => {
-  console.error("Error executing toolbox:", err);
-  process.exit(1);
-});
-`
-
-type scriptData struct {
-	Name              string
-	PrebuiltNamesJSON string
-	ToolsFileName     string
-}
-
-func generateShellScriptContent(name string, config serverConfig, toolsFileName string) (string, error) {
-	prebuiltJSON, _ := json.Marshal(config.prebuiltConfigs)
-
-	data := scriptData{
-		Name:              name,
-		PrebuiltNamesJSON: string(prebuiltJSON),
-		ToolsFileName:     toolsFileName,
-	}
-
-	tmpl, err := template.New("script").Parse(nodeScriptTemplate)
-	if err != nil {
-		return "", fmt.Errorf("error parsing script template: %w", err)
-	}
-
-	var buf strings.Builder
-	if err := tmpl.Execute(&buf, data); err != nil {
-		return "", fmt.Errorf("error executing script template: %w", err)
-	}
-
-	return buf.String(), nil
-}
-
-func formatParameters(params []Parameter) (string, error) {
-	if len(params) == 0 {
-		return "", nil
-	}
-
-	properties := make(map[string]interface{})
-	var required []string
-
-	for _, p := range params {
-		paramMap := map[string]interface{}{
-			"type":        p.Type,
-			"description": p.Description,
-		}
-		if p.Default != nil {
-			paramMap["default"] = p.Default
-		}
-		properties[p.Name] = paramMap
-		if p.Required {
-			required = append(required, p.Name)
-		}
-	}
-
-	schema := map[string]interface{}{
-		"type":       "object",
-		"properties": properties,
-	}
-	if len(required) > 0 {
-		schema["required"] = required
-	}
-
-	schemaJSON, err := json.MarshalIndent(schema, "", "  ")
-	if err != nil {
-		return "", fmt.Errorf("error generating parameters schema: %w", err)
-	}
-
-	return fmt.Sprintf("## Parameters\n\n```json\n%s\n```", string(schemaJSON)), nil
-}
-
-func generateFilteredConfig(toolsFile, toolName string) ([]byte, error) {
-	data, err := os.ReadFile(toolsFile)
-	if err != nil {
-		return nil, fmt.Errorf("error reading %s: %w", toolsFile, err)
-	}
-	var cfg Config
-	if err := yaml.Unmarshal(data, &cfg); err != nil {
-		return nil, fmt.Errorf("error parsing YAML from %s: %w", toolsFile, err)
-	}
-
-	if _, ok := cfg.Tools[toolName]; !ok {
-		return nil, nil // Tool not found in this file
-	}
-
-	filteredCfg := Config{
-		Tools: map[string]map[string]interface{}{
-			toolName: cfg.Tools[toolName],
-		},
-	}
-
-	// Add relevant source if exists
-	if src, ok := cfg.Tools[toolName]["source"].(string); ok && src != "" {
-		if sourceData, exists := cfg.Sources[src]; exists {
-			if filteredCfg.Sources == nil {
-				filteredCfg.Sources = make(map[string]interface{})
-			}
-			filteredCfg.Sources[src] = sourceData
-		}
-	}
-
-	filteredData, err := yaml.Marshal(filteredCfg)
-	if err != nil {
-		return nil, fmt.Errorf("error marshaling filtered tools for %s: %w", toolName, err)
-	}
-	return filteredData, nil
-}

internal/cli/skills/generator_test.go

@@ -1,300 +0,0 @@
-// Copyright 2026 Google LLC
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//     http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
-
-package skills
-
-import (
-	"os"
-	"path/filepath"
-	"strings"
-	"testing"
-
-	"github.com/goccy/go-yaml"
-	"github.com/google/go-cmp/cmp"
-)
-
-func TestFormatParameters(t *testing.T) {
-	tests := []struct {
-		name         string
-		params       []Parameter
-		wantContains []string
-		wantErr      bool
-	}{
-		{
-			name:         "empty parameters",
-			params:       []Parameter{},
-			wantContains: []string{""},
-		},
-		{
-			name: "single required string parameter",
-			params: []Parameter{
-				{
-					Name:        "param1",
-					Description: "A test parameter",
-					Type:        "string",
-					Required:    true,
-				},
-			},
-			wantContains: []string{
-				"## Parameters",
-				"```json",
-				`"type": "object"`,
-				`"properties": {`,
-				`"param1": {`,
-				`"type": "string"`,
-				`"description": "A test parameter"`,
-				`"required": [`,
-				`"param1"`,
-			},
-		},
-		{
-			name: "mixed parameters with defaults",
-			params: []Parameter{
-				{
-					Name:        "param1",
-					Description: "Param 1",
-					Type:        "string",
-					Required:    true,
-				},
-				{
-					Name:        "param2",
-					Description: "Param 2",
-					Type:        "integer",
-					Default:     42,
-					Required:    false,
-				},
-			},
-			wantContains: []string{
-				`"param1": {`,
-				`"param2": {`,
-				`"default": 42`,
-				`"required": [`,
-				`"param1"`,
-			},
-		},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			got, err := formatParameters(tt.params)
-			if (err != nil) != tt.wantErr {
-				t.Errorf("formatParameters() error = %v, wantErr %v", err, tt.wantErr)
-				return
-			}
-			if tt.wantErr {
-				return
-			}
-
-			if len(tt.params) == 0 {
-				if got != "" {
-					t.Errorf("formatParameters() = %v, want empty string", got)
-				}
-				return
-			}
-
-			for _, want := range tt.wantContains {
-				if !strings.Contains(got, want) {
-					t.Errorf("formatParameters() result missing expected string: %s\nGot:\n%s", want, got)
-				}
-			}
-		})
-	}
-}
-
-func TestGenerateSkillMarkdown(t *testing.T) {
-	tools := map[string]Tool{
-		"tool1": {
-			Name:        "tool1",
-			Description: "First tool",
-			Parameters: []Parameter{
-				{Name: "p1", Type: "string", Description: "d1", Required: true},
-			},
-		},
-	}
-
-	got, err := generateSkillMarkdown("MySkill", "My Description", tools)
-	if err != nil {
-		t.Fatalf("generateSkillMarkdown() error = %v", err)
-	}
-
-	expectedSubstrings := []string{
-		"name: MySkill",
-		"description: My Description",
-		"# tool1",
-		"First tool",
-		"## Parameters",
-		"node scripts/tool1.js '{\"<param_name>\": \"<param_value>\"}'",
-	}
-
-	for _, s := range expectedSubstrings {
-		if !strings.Contains(got, s) {
-			t.Errorf("generateSkillMarkdown() missing substring %q", s)
-		}
-	}
-}
-
-func TestGenerateShellScriptContent(t *testing.T) {
-	tests := []struct {
-		name          string
-		toolName      string
-		config        serverConfig
-		toolsFileName string
-		wantContains  []string
-	}{
-		{
-			name:     "basic script",
-			toolName: "test-tool",
-			config: serverConfig{
-				prebuiltConfigs: []string{},
-			},
-			toolsFileName: "",
-			wantContains: []string{
-				`const toolName = "test-tool";`,
-				`const prebuiltNames = [];`,
-				`const toolsFileName = "";`,
-				`const toolboxArgs = [...configArgs, "invoke", toolName, ...args];`,
-			},
-		},
-		{
-			name:     "script with prebuilts and tools file",
-			toolName: "complex-tool",
-			config: serverConfig{
-				prebuiltConfigs: []string{"pre1", "pre2"},
-			},
-			toolsFileName: "tools.yaml",
-			wantContains: []string{
-				`const toolName = "complex-tool";`,
-				`const prebuiltNames = ["pre1","pre2"];`,
-				`const toolsFileName = "tools.yaml";`,
-				`configArgs.push("--prebuilt", name);`,
-				`configArgs.push("--tools-file", path.join(__dirname, "..", "assets", toolsFileName));`,
-			},
-		},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			got, err := generateShellScriptContent(tt.toolName, tt.config, tt.toolsFileName)
-			if err != nil {
-				t.Fatalf("generateShellScriptContent() error = %v", err)
-			}
-
-			for _, s := range tt.wantContains {
-				if !strings.Contains(got, s) {
-					t.Errorf("generateShellScriptContent() missing substring %q\nGot:\n%s", s, got)
-				}
-			}
-		})
-	}
-}
-
-func TestGenerateFilteredConfig(t *testing.T) {
-	// Setup temporary directory and file
-	tmpDir := t.TempDir()
-	toolsFile := filepath.Join(tmpDir, "tools.yaml")
-
-	configContent := `
-sources:
-  src1:
-    type: "postgres"
-    connection_string: "conn1"
-  src2:
-    type: "mysql"
-    connection_string: "conn2"
-tools:
-  tool1:
-    source: "src1"
-    query: "SELECT 1"
-  tool2:
-    source: "src2"
-    query: "SELECT 2"
-  tool3:
-    type: "http" # No source
-`
-	if err := os.WriteFile(toolsFile, []byte(configContent), 0644); err != nil {
-		t.Fatalf("Failed to create temp tools file: %v", err)
-	}
-
-	tests := []struct {
-		name     string
-		toolName string
-		wantCfg  Config
-		wantErr  bool
-		wantNil  bool
-	}{
-		{
-			name:     "tool with source",
-			toolName: "tool1",
-			wantCfg: Config{
-				Sources: map[string]interface{}{
-					"src1": map[string]interface{}{
-						"type":              "postgres",
-						"connection_string": "conn1",
-					},
-				},
-				Tools: map[string]map[string]interface{}{
-					"tool1": {
-						"source": "src1",
-						"query":  "SELECT 1",
-					},
-				},
-			},
-		},
-		{
-			name:     "tool without source",
-			toolName: "tool3",
-			wantCfg: Config{
-				Tools: map[string]map[string]interface{}{
-					"tool3": {
-						"type": "http",
-					},
-				},
-			},
-		},
-		{
-			name:     "non-existent tool",
-			toolName: "missing-tool",
-			wantNil:  true,
-		},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			gotBytes, err := generateFilteredConfig(toolsFile, tt.toolName)
-			if (err != nil) != tt.wantErr {
-				t.Errorf("generateFilteredConfig() error = %v, wantErr %v", err, tt.wantErr)
-				return
-			}
-			if tt.wantErr {
-				return
-			}
-
-			if tt.wantNil {
-				if gotBytes != nil {
-					t.Errorf("generateFilteredConfig() expected nil, got %s", string(gotBytes))
-				}
-				return
-			}
-
-			var gotCfg Config
-			if err := yaml.Unmarshal(gotBytes, &gotCfg); err != nil {
-				t.Errorf("Failed to unmarshal result: %v", err)
-			}
-
-			if diff := cmp.Diff(tt.wantCfg, gotCfg); diff != "" {
-				t.Errorf("generateFilteredConfig() mismatch (-want +got):\n%s", diff)
-			}
-		})
-	}
-}

internal/log/log.go

@@ -22,18 +22,6 @@ import (
 	"strings"
 )
 
-// NewLogger creates a new logger based on the provided format and level.
-func NewLogger(format, level string, out, err io.Writer) (Logger, error) {
-	switch strings.ToLower(format) {
-	case "json":
-		return NewStructuredLogger(out, err, level)
-	case "standard":
-		return NewStdLogger(out, err, level)
-	default:
-		return nil, fmt.Errorf("logging format invalid: %s", format)
-	}
-}
-
 // StdLogger is the standard logger
 type StdLogger struct {
 	outLogger *slog.Logger

internal/sources/mongodb/mongodb.go

@@ -23,9 +23,9 @@ import (
 	"github.com/goccy/go-yaml"
 	"github.com/googleapis/genai-toolbox/internal/sources"
 	"github.com/googleapis/genai-toolbox/internal/util"
-	"go.mongodb.org/mongo-driver/v2/bson"
+	"go.mongodb.org/mongo-driver/bson"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
-	"go.mongodb.org/mongo-driver/v2/mongo/options"
+	"go.mongodb.org/mongo-driver/mongo/options"
 	"go.opentelemetry.io/otel/trace"
 )
 
@@ -148,7 +148,7 @@ func (s *Source) Aggregate(ctx context.Context, pipelineString string, canonical
 	return res, err
 }
 
-func (s *Source) Find(ctx context.Context, filterString, database, collection string, opts *options.FindOptionsBuilder) ([]any, error) {
+func (s *Source) Find(ctx context.Context, filterString, database, collection string, opts *options.FindOptions) ([]any, error) {
 	var filter = bson.D{}
 	err := bson.UnmarshalExtJSON([]byte(filterString), false, &filter)
 	if err != nil {
@@ -163,7 +163,7 @@ func (s *Source) Find(ctx context.Context, filterString, database, collection st
 	return parseData(ctx, cur)
 }
 
-func (s *Source) FindOne(ctx context.Context, filterString, database, collection string, opts *options.FindOneOptionsBuilder) ([]any, error) {
+func (s *Source) FindOne(ctx context.Context, filterString, database, collection string, opts *options.FindOneOptions) ([]any, error) {
 	var filter = bson.D{}
 	err := bson.UnmarshalExtJSON([]byte(filterString), false, &filter)
 	if err != nil {
@@ -233,7 +233,7 @@ func (s *Source) UpdateMany(ctx context.Context, filterString string, canonical
 		return nil, fmt.Errorf("unable to unmarshal update string: %w", err)
 	}
 
-	res, err := s.MongoClient().Database(database).Collection(collection).UpdateMany(ctx, filter, update, options.UpdateMany().SetUpsert(upsert))
+	res, err := s.MongoClient().Database(database).Collection(collection).UpdateMany(ctx, filter, update, options.Update().SetUpsert(upsert))
 	if err != nil {
 		return nil, fmt.Errorf("error updating collection: %w", err)
 	}
@@ -252,7 +252,7 @@ func (s *Source) UpdateOne(ctx context.Context, filterString string, canonical b
 		return nil, fmt.Errorf("unable to unmarshal update string: %w", err)
 	}
 
-	res, err := s.MongoClient().Database(database).Collection(collection).UpdateOne(ctx, filter, update, options.UpdateOne().SetUpsert(upsert))
+	res, err := s.MongoClient().Database(database).Collection(collection).UpdateOne(ctx, filter, update, options.Update().SetUpsert(upsert))
 	if err != nil {
 		return nil, fmt.Errorf("error updating collection: %w", err)
 	}
@@ -266,7 +266,7 @@ func (s *Source) DeleteMany(ctx context.Context, filterString, database, collect
 		return nil, err
 	}
 
-	res, err := s.MongoClient().Database(database).Collection(collection).DeleteMany(ctx, filter, options.DeleteMany())
+	res, err := s.MongoClient().Database(database).Collection(collection).DeleteMany(ctx, filter, options.Delete())
 	if err != nil {
 		return nil, err
 	}
@@ -284,7 +284,7 @@ func (s *Source) DeleteOne(ctx context.Context, filterString, database, collecti
 		return nil, err
 	}
 
-	res, err := s.MongoClient().Database(database).Collection(collection).DeleteOne(ctx, filter, options.DeleteOne())
+	res, err := s.MongoClient().Database(database).Collection(collection).DeleteOne(ctx, filter, options.Delete())
 	if err != nil {
 		return nil, err
 	}
@@ -303,7 +303,7 @@ func initMongoDBClient(ctx context.Context, tracer trace.Tracer, name, uri strin
 
 	// Create a new MongoDB client
 	clientOpts := options.Client().ApplyURI(uri).SetAppName(userAgent)
-	client, err := mongo.Connect(clientOpts)
+	client, err := mongo.Connect(ctx, clientOpts)
 	if err != nil {
 		return nil, fmt.Errorf("unable to create MongoDB client: %w", err)
 	}

internal/tools/mongodb/mongodbaggregate/mongodbaggregate.go

@@ -21,7 +21,7 @@ import (
 	"github.com/goccy/go-yaml"
 	"github.com/googleapis/genai-toolbox/internal/embeddingmodels"
 	"github.com/googleapis/genai-toolbox/internal/util/parameters"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
 
 	"github.com/googleapis/genai-toolbox/internal/sources"
 	"github.com/googleapis/genai-toolbox/internal/tools"

internal/tools/mongodb/mongodbdeletemany/mongodbdeletemany.go

@@ -21,7 +21,7 @@ import (
 	"github.com/goccy/go-yaml"
 	"github.com/googleapis/genai-toolbox/internal/embeddingmodels"
 	"github.com/googleapis/genai-toolbox/internal/util/parameters"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
 
 	"github.com/googleapis/genai-toolbox/internal/sources"
 	"github.com/googleapis/genai-toolbox/internal/tools"

internal/tools/mongodb/mongodbdeleteone/mongodbdeleteone.go

@@ -21,7 +21,7 @@ import (
 	"github.com/goccy/go-yaml"
 	"github.com/googleapis/genai-toolbox/internal/embeddingmodels"
 	"github.com/googleapis/genai-toolbox/internal/util/parameters"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
 
 	"github.com/googleapis/genai-toolbox/internal/sources"
 	"github.com/googleapis/genai-toolbox/internal/tools"

internal/tools/mongodb/mongodbfind/mongodbfind.go

@@ -22,9 +22,9 @@ import (
 	"github.com/googleapis/genai-toolbox/internal/embeddingmodels"
 	"github.com/googleapis/genai-toolbox/internal/util"
 	"github.com/googleapis/genai-toolbox/internal/util/parameters"
-	"go.mongodb.org/mongo-driver/v2/bson"
+	"go.mongodb.org/mongo-driver/bson"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
-	"go.mongodb.org/mongo-driver/v2/mongo/options"
+	"go.mongodb.org/mongo-driver/mongo/options"
 
 	"github.com/googleapis/genai-toolbox/internal/sources"
 	"github.com/googleapis/genai-toolbox/internal/tools"
@@ -48,7 +48,7 @@ func newConfig(ctx context.Context, name string, decoder *yaml.Decoder) (tools.T
 
 type compatibleSource interface {
 	MongoClient() *mongo.Client
-	Find(context.Context, string, string, string, *options.FindOptionsBuilder) ([]any, error)
+	Find(context.Context, string, string, string, *options.FindOptions) ([]any, error)
 }
 
 type Config struct {
@@ -118,7 +118,7 @@ type Tool struct {
 	mcpManifest tools.McpManifest
 }
 
-func getOptions(ctx context.Context, sortParameters parameters.Parameters, projectPayload string, limit int64, paramsMap map[string]any) (*options.FindOptionsBuilder, error) {
+func getOptions(ctx context.Context, sortParameters parameters.Parameters, projectPayload string, limit int64, paramsMap map[string]any) (*options.FindOptions, error) {
 	logger, err := util.LoggerFromContext(ctx)
 	if err != nil {
 		panic(err)

internal/tools/mongodb/mongodbfindone/mongodbfindone.go

@@ -21,9 +21,9 @@ import (
 	"github.com/goccy/go-yaml"
 	"github.com/googleapis/genai-toolbox/internal/embeddingmodels"
 	"github.com/googleapis/genai-toolbox/internal/util/parameters"
-	"go.mongodb.org/mongo-driver/v2/bson"
+	"go.mongodb.org/mongo-driver/bson"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
-	"go.mongodb.org/mongo-driver/v2/mongo/options"
+	"go.mongodb.org/mongo-driver/mongo/options"
 
 	"github.com/googleapis/genai-toolbox/internal/sources"
 	"github.com/googleapis/genai-toolbox/internal/tools"
@@ -47,7 +47,7 @@ func newConfig(ctx context.Context, name string, decoder *yaml.Decoder) (tools.T
 
 type compatibleSource interface {
 	MongoClient() *mongo.Client
-	FindOne(context.Context, string, string, string, *options.FindOneOptionsBuilder) ([]any, error)
+	FindOne(context.Context, string, string, string, *options.FindOneOptions) ([]any, error)
 }
 
 type Config struct {

internal/tools/mongodb/mongodbinsertmany/mongodbinsertmany.go

@@ -23,7 +23,7 @@ import (
 	"github.com/googleapis/genai-toolbox/internal/sources"
 	"github.com/googleapis/genai-toolbox/internal/tools"
 	"github.com/googleapis/genai-toolbox/internal/util/parameters"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
 )
 
 const resourceType string = "mongodb-insert-many"

internal/tools/mongodb/mongodbinsertone/mongodbinsertone.go

@@ -23,7 +23,7 @@ import (
 	"github.com/googleapis/genai-toolbox/internal/sources"
 	"github.com/googleapis/genai-toolbox/internal/tools"
 	"github.com/googleapis/genai-toolbox/internal/util/parameters"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
 )
 
 const resourceType string = "mongodb-insert-one"

internal/tools/mongodb/mongodbupdatemany/mongodbupdatemany.go

@@ -23,7 +23,7 @@ import (
 	"github.com/googleapis/genai-toolbox/internal/sources"
 	"github.com/googleapis/genai-toolbox/internal/tools"
 	"github.com/googleapis/genai-toolbox/internal/util/parameters"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
 )
 
 const resourceType string = "mongodb-update-many"

internal/tools/mongodb/mongodbupdateone/mongodbupdateone.go

@@ -23,7 +23,7 @@ import (
 	"github.com/googleapis/genai-toolbox/internal/sources"
 	"github.com/googleapis/genai-toolbox/internal/tools"
 	"github.com/googleapis/genai-toolbox/internal/util/parameters"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
 )
 
 const resourceType string = "mongodb-update-one"

internal/util/errors.go

@@ -0,0 +1,60 @@
+// Copyright 2026 Google LLC
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//	http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+package util
+
+import "fmt"
+
+type ErrorCategory string
+
+const (
+	CategoryAgent  ErrorCategory = "AGENT_ERROR"
+	CategoryServer ErrorCategory = "SERVER_ERROR"
+)
+
+// ToolboxError is the interface all custom errors must satisfy
+type ToolboxError interface {
+	error
+	Category() ErrorCategory
+}
+
+// Agent Errors
+type AgentError struct {
+	Msg   string
+	Cause error
+}
+
+func (e *AgentError) Error() string { return e.Msg }
+
+func (e *AgentError) Category() ErrorCategory { return CategoryAgent }
+
+func (e *AgentError) Unwrap() error { return e.Cause }
+
+func NewAgentError(msg string, args ...any) *AgentError {
+	return &AgentError{Msg: fmt.Sprintf(msg, args...)}
+}
+
+// Server Errors
+type ServerError struct {
+	Msg   string
+	Cause error
+}
+
+func (e *ServerError) Error() string { return fmt.Sprintf("%s: %v", e.Msg, e.Cause) }
+
+func (e *ServerError) Category() ErrorCategory { return CategoryServer }
+
+func (e *ServerError) Unwrap() error { return e.Cause }
+
+func NewServerError(msg string, cause error) *ServerError {
+	return &ServerError{Msg: msg, Cause: cause}
+}

tests/mongodb/mongodb_integration_test.go

@@ -28,8 +28,8 @@ import (
 
 	"github.com/googleapis/genai-toolbox/internal/testutils"
 	"github.com/googleapis/genai-toolbox/tests"
-	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/mongo"
-	"go.mongodb.org/mongo-driver/v2/mongo/options"
+	"go.mongodb.org/mongo-driver/mongo/options"
 )
 
 var (
@@ -55,7 +55,7 @@ func getMongoDBVars(t *testing.T) map[string]any {
 
 func initMongoDbDatabase(ctx context.Context, uri, database string) (*mongo.Database, error) {
 	// Create a new mongodb Database
-	client, err := mongo.Connect(options.Client().ApplyURI(uri))
+	client, err := mongo.Connect(ctx, options.Client().ApplyURI(uri))
 	if err != nil {
 		return nil, fmt.Errorf("unable to connect to mongodb: %s", err)
 	}