Feature/drs server

.github/workflows/ci.yaml

@@ -0,0 +1,36 @@
+name: Data Client CI
+
+on:
+  pull_request:
+  push:
+  workflow_dispatch:
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  lint-and-test:
+    name: Lint and Unit Tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Go
+        uses: actions/setup-go@v5
+        with:
+          go-version-file: go.mod
+          cache: true
+
+      - name: Download dependencies
+        run: GOTOOLCHAIN=auto go mod download
+
+      - name: Run go vet
+        run: GOTOOLCHAIN=auto go vet ./...
+
+      - name: Run unit tests
+        run: GOTOOLCHAIN=auto go test -v ./...

.gitignore

@@ -28,4 +28,8 @@
 # Build artifacts
 /build/
 /bin/
-checksums.txt
+checksums.txt
+# Local caches and binaries
+/.gocache/
+/.tmp/
+/data-client

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "ga4gh/data-repository-service-schemas"]
+	path = ga4gh/data-repository-service-schemas
+	url = https://github.com/kellrott/data-repository-service-schemas.git
+	branch = feature/get-by-checksum

Makefile

@@ -14,6 +14,9 @@ BIN_DIR := ./bin
 COVERAGE_THRESHOLD := 30
 PACKAGE_COVERAGE_THRESHOLD := 20
 
+# OpenAPI generation now lives in syfon.
+SYFON_DIR ?= ../syfon
+
 # --- Targets ---
 
 .PHONY: all build test test-coverage coverage-html coverage-check generate tidy clean help
@@ -55,6 +58,26 @@ generate:
 	@echo "--> Running code generation (go generate)..."
 	@go generate ./...
 
+## gen: Generates Go models from OpenAPI specs
+gen:
+	@set -euo pipefail; \
+	if [[ ! -d "$(SYFON_DIR)" ]]; then \
+	  echo "ERROR: syfon repo not found at $(SYFON_DIR)"; \
+	  exit 1; \
+	fi; \
+	echo "--> OpenAPI generation is centralized in syfon"; \
+	$(MAKE) -C "$(SYFON_DIR)" gen
+
+.PHONY: gen-internal
+gen-internal:
+	@set -euo pipefail; \
+	if [[ ! -d "$(SYFON_DIR)" ]]; then \
+	  echo "ERROR: syfon repo not found at $(SYFON_DIR)"; \
+	  exit 1; \
+	fi; \
+	echo "--> Internal model generation is centralized in syfon"; \
+	$(MAKE) -C "$(SYFON_DIR)" gen-internal
+
 ## tidy: Cleans up module dependencies and formats go files
 tidy:
 	@echo "--> Tidying go.mod and formatting files..."
@@ -66,4 +89,4 @@ clean:
 	@echo "--> Cleaning up..."
 	@rm -f $(BIN_DIR)/$(TARGET_NAME)
 	@rm -f coverage.out coverage.html
-
+	@rm -rf .tmp

cmd/auth.go

@@ -32,14 +32,14 @@ func init() {
 				log.Fatalf("Fatal NewGen3Interface error: %s\n", err)
 			}
 
-			resourceAccess, err := g3i.Fence().CheckPrivileges(context.Background())
+			resourceAccess, err := g3i.FenceClient().CheckPrivileges(context.Background())
 			if err != nil {
 				g3i.Logger().Fatalf("Fatal authentication error: %s\n", err)
 			} else {
 				if len(resourceAccess) == 0 {
-					g3i.Logger().Printf("\nYou don't currently have access to any resources at %s\n", g3i.GetCredential().APIEndpoint)
+					g3i.Logger().Printf("\nYou don't currently have access to any resources at %s\n", g3i.Credentials().Current().APIEndpoint)
 				} else {
-					g3i.Logger().Printf("\nYou have access to the following resource(s) at %s:\n", g3i.GetCredential().APIEndpoint)
+					g3i.Logger().Printf("\nYou have access to the following resource(s) at %s:\n", g3i.Credentials().Current().APIEndpoint)
 
 					// Sort by resource name
 					resources := make([]string, 0, len(resourceAccess))

cmd/collaborator.go

@@ -14,26 +14,13 @@ import (
 	"gopkg.in/yaml.v3"
 )
 
-var collaboratorCmd = &cobra.Command{
-	Use:   "collaborator",
+var collaboratorsCmd = &cobra.Command{
+	Use:   "collaborators",
 	Short: "Manage collaborators and access requests",
 }
 
 var emailRegex = regexp.MustCompile(`^[a-z0-9._%+\-]+@[a-z0-9.\-]+\.[a-z]{2,}$`)
 
-func validateProjectAndUser(projectID, username string) error {
-	if !emailRegex.MatchString(strings.ToLower(username)) {
-		return fmt.Errorf("invalid username '%s': must be a valid email address", username)
-	}
-
-	parts := strings.Split(projectID, "-")
-	if len(parts) != 2 || parts[0] == "" || parts[1] == "" {
-		return fmt.Errorf("invalid project_id '%s': must be in the form 'program-project'", projectID)
-	}
-
-	return nil
-}
-
 func printRequest(r requestor.Request) {
 	b, err := yaml.Marshal(r)
 	if err != nil {
@@ -43,35 +30,37 @@ func printRequest(r requestor.Request) {
 	fmt.Println(string(b))
 }
 
-func getRequestorClient() (requestor.RequestorInterface, func()) {
-	if profile == "" {
-		fmt.Println("Error: profile is required. Please specify a profile using the --profile flag.")
+func getRequestorClient(localProfile string) (requestor.RequestorInterface, func()) {
+	if localProfile == "" {
+		fmt.Println("Error: profile is required.")
 		os.Exit(1)
 	}
 
 	// Initialize logger
-	logger, logCloser := logs.New(profile)
+	logger, logCloser := logs.New(localProfile)
 
-	// Initialize Gen3Interface handles selective initialization
-	g3i, err := g3client.NewGen3Interface(profile, logger, g3client.WithClients(g3client.RequestorClient))
+	// Initialize base Gen3 interface and build requestor client from it.
+	g3i, err := g3client.NewGen3Interface(localProfile, logger)
 	if err != nil {
 		fmt.Printf("Error accessing Gen3: %v\n", err)
 		logCloser()
 		os.Exit(1)
 	}
 
-	return g3i.Requestor(), logCloser
+	return requestor.NewRequestorClient(g3i, g3i.Credentials().Current()), logCloser
 }
 
 var collaboratorListCmd = &cobra.Command{
-	Use:   "ls",
+	Use:   "ls [profile]",
 	Short: "List requests",
+	Args:  cobra.ExactArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
+		p := args[0]
 		mine, _ := cmd.Flags().GetBool("mine")
 		active, _ := cmd.Flags().GetBool("active")
 		username, _ := cmd.Flags().GetString("username")
 
-		client, closer := getRequestorClient()
+		client, closer := getRequestorClient(p)
 		defer closer()
 
 		requests, err := client.ListRequests(cmd.Context(), mine, active, username)
@@ -87,10 +76,12 @@ var collaboratorListCmd = &cobra.Command{
 }
 
 var collaboratorPendingCmd = &cobra.Command{
-	Use:   "pending",
+	Use:   "pending [profile]",
 	Short: "List pending requests",
+	Args:  cobra.ExactArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
-		client, closer := getRequestorClient()
+		p := args[0]
+		client, closer := getRequestorClient(p)
 		defer closer()
 
 		// Fetch all requests
@@ -110,22 +101,26 @@ var collaboratorPendingCmd = &cobra.Command{
 }
 
 var collaboratorAddUserCmd = &cobra.Command{
-	Use:   "add [project_id] [username]",
+	Use:   "add [profile] [email] [program] [project]",
 	Short: "Add a user to a project",
-	Args: func(cmd *cobra.Command, args []string) error {
-		if err := cobra.ExactArgs(2)(cmd, args); err != nil {
-			return err
-		}
-		return validateProjectAndUser(args[0], args[1])
-	},
+	Args:  cobra.ExactArgs(4),
 	Run: func(cmd *cobra.Command, args []string) {
-		projectID := args[0]
+		p := args[0]
 		username := args[1]
+		program := args[2]
+		project := args[3]
+		projectID := fmt.Sprintf("%s-%s", program, project)
+
+		if !emailRegex.MatchString(strings.ToLower(username)) {
+			fmt.Printf("Error: invalid email address '%s'\n", username)
+			os.Exit(1)
+		}
+
 		write, _ := cmd.Flags().GetBool("write")
 		guppy, _ := cmd.Flags().GetBool("guppy")
 		approve, _ := cmd.Flags().GetBool("approve")
 
-		client, closer := getRequestorClient()
+		client, closer := getRequestorClient(p)
 		defer closer()
 
 		reqs, err := client.AddUser(cmd.Context(), projectID, username, write, guppy)
@@ -156,20 +151,24 @@ var collaboratorAddUserCmd = &cobra.Command{
 }
 
 var collaboratorRemoveUserCmd = &cobra.Command{
-	Use:   "rm [project_id] [username]",
+	Use:   "rm [profile] [email] [program] [project]",
 	Short: "Remove a user from a project",
-	Args: func(cmd *cobra.Command, args []string) error {
-		if err := cobra.ExactArgs(2)(cmd, args); err != nil {
-			return err
-		}
-		return validateProjectAndUser(args[0], args[1])
-	},
+	Args:  cobra.ExactArgs(4),
 	Run: func(cmd *cobra.Command, args []string) {
-		projectID := args[0]
+		p := args[0]
 		username := args[1]
+		program := args[2]
+		project := args[3]
+		projectID := fmt.Sprintf("%s-%s", program, project)
+
+		if !emailRegex.MatchString(strings.ToLower(username)) {
+			fmt.Printf("Error: invalid email address '%s'\n", username)
+			os.Exit(1)
+		}
+
 		approve, _ := cmd.Flags().GetBool("approve")
 
-		client, closer := getRequestorClient()
+		client, closer := getRequestorClient(p)
 		defer closer()
 
 		reqs, err := client.RemoveUser(cmd.Context(), projectID, username)
@@ -199,13 +198,14 @@ var collaboratorRemoveUserCmd = &cobra.Command{
 }
 
 var collaboratorApproveCmd = &cobra.Command{
-	Use:   "approve [request_id]",
+	Use:   "approve [profile] [request_id]",
 	Short: "Approve a request (sign it)",
-	Args:  cobra.ExactArgs(1),
+	Args:  cobra.ExactArgs(2),
 	Run: func(cmd *cobra.Command, args []string) {
-		requestID := args[0]
+		p := args[0]
+		requestID := args[1]
 
-		client, closer := getRequestorClient()
+		client, closer := getRequestorClient(p)
 		defer closer()
 
 		req, err := client.UpdateRequest(cmd.Context(), requestID, "SIGNED")
@@ -220,15 +220,16 @@ var collaboratorApproveCmd = &cobra.Command{
 }
 
 var collaboratorUpdateCmd = &cobra.Command{
-	Use:    "update [request_id] [status]",
+	Use:    "update [profile] [request_id] [status]",
 	Short:  "Update a request status",
 	Hidden: true,
-	Args:   cobra.ExactArgs(2),
+	Args:   cobra.ExactArgs(3),
 	Run: func(cmd *cobra.Command, args []string) {
-		requestID := args[0]
-		status := args[1]
+		p := args[0]
+		requestID := args[1]
+		status := args[2]
 
-		client, closer := getRequestorClient()
+		client, closer := getRequestorClient(p)
 		defer closer()
 
 		req, err := client.UpdateRequest(cmd.Context(), requestID, status)
@@ -242,13 +243,13 @@ var collaboratorUpdateCmd = &cobra.Command{
 }
 
 func init() {
-	RootCmd.AddCommand(collaboratorCmd)
-	collaboratorCmd.AddCommand(collaboratorListCmd)
-	collaboratorCmd.AddCommand(collaboratorPendingCmd)
-	collaboratorCmd.AddCommand(collaboratorAddUserCmd)
-	collaboratorCmd.AddCommand(collaboratorRemoveUserCmd)
-	collaboratorCmd.AddCommand(collaboratorApproveCmd)
-	collaboratorCmd.AddCommand(collaboratorUpdateCmd)
+	RootCmd.AddCommand(collaboratorsCmd)
+	collaboratorsCmd.AddCommand(collaboratorListCmd)
+	collaboratorsCmd.AddCommand(collaboratorPendingCmd)
+	collaboratorsCmd.AddCommand(collaboratorAddUserCmd)
+	collaboratorsCmd.AddCommand(collaboratorRemoveUserCmd)
+	collaboratorsCmd.AddCommand(collaboratorApproveCmd)
+	collaboratorsCmd.AddCommand(collaboratorUpdateCmd)
 
 	collaboratorListCmd.Flags().Bool("mine", false, "List my requests")
 	collaboratorListCmd.Flags().Bool("active", false, "List only active requests")
@@ -259,6 +260,4 @@ func init() {
 	collaboratorAddUserCmd.Flags().BoolP("approve", "a", false, "Automatically approve the requests")
 
 	collaboratorRemoveUserCmd.Flags().BoolP("approve", "a", false, "Automatically approve the revoke requests")
-
-	collaboratorCmd.PersistentFlags().StringVar(&profile, "profile", "", "Specify profile to use")
 }

cmd/configure.go

@@ -51,7 +51,7 @@ func init() {
 			}
 
 			g3i := g3client.NewGen3InterfaceFromCredential(cred, logger, g3client.WithClients())
-			err := g3i.ExportCredential(context.Background(), cred)
+			err := g3i.Credentials().Export(context.Background(), cred)
 			if err != nil {
 				logger.Println(err.Error())
 			}