config can be provided before command

download/download.go

@@ -96,14 +96,17 @@ type File struct {
 
 // Download function downloads files from the SDA by using the
 // download's service APIs
-func Download(args []string) error {
+func Download(args []string, configPathF string) error {
 	// Call ParseArgs to take care of all the flag parsing
 	err := helpers.ParseArgs(args, Args)
 	if err != nil {
 		return fmt.Errorf("failed parsing arguments, reason: %v", err)
 	}
+	if configPathF == "" {
+		configPathF = *configPath
+	}
 
-	if *datasetID == "" || *URL == "" || *configPath == "" {
+	if *datasetID == "" || *URL == "" || configPathF == "" {
 		return fmt.Errorf("missing required arguments, dataset, config and url are required")
 	}
 
@@ -136,7 +139,7 @@ func Download(args []string) error {
 	}
 
 	// Get the configuration file or the .sda-cli-session
-	config, err := helpers.GetAuth(*configPath)
+	config, err := helpers.GetAuth(configPathF)
 	if err != nil {
 		return err
 	}

htsget/htsget.go

@@ -73,19 +73,22 @@ type htsgetResponse struct {
 
 // Htsget function downloads the files included in the urls_list.txt file.
 // The argument can be a local file or a url to an S3 folder
-func Htsget(args []string) error {
+func Htsget(args []string, configPathF string) error {
 
 	// Call ParseArgs to take care of all the flag parsing
 	err := helpers.ParseArgs(args, Args)
 	if err != nil {
 		return fmt.Errorf("failed parsing arguments, reason: %v", err)
 	}
+	if configPathF == "" {
+		configPathF = *configPath
+	}
 
 	if *datasetID == "" || *fileName == "" || *htsgetHost == "" || *publicKeyFile == "" {
 		return fmt.Errorf("missing required arguments, dataset, filename, host and key are required")
 	}
 
-	config, err := helpers.GetAuth(*configPath)
+	config, err := helpers.GetAuth(configPathF)
 	if err != nil {
 		return err
 	}

list/list.go

@@ -52,20 +52,23 @@ var bytesFormat = Args.Bool("bytes", false, "Print file sizes in bytes (not huma
 var dataset = Args.String("dataset", "", "List all files in the specified dataset.")
 
 // List function lists the contents of an s3
-func List(args []string) error {
+func List(args []string, configPathF string) error {
 	// Call ParseArgs to take care of all the flag parsing
 	err := helpers.ParseArgs(args, Args)
 	if err != nil {
 		return fmt.Errorf("failed parsing arguments, reason: %v", err)
 	}
+	if configPathF == "" {
+		configPathF = *configPath
+	}
 
 	prefix := ""
 	if len(Args.Args()) == 1 {
 		prefix = Args.Args()[0]
 	}
 
 	// // Get the configuration file or the .sda-cli-session
-	config, err := helpers.GetAuth(*configPath)
+	config, err := helpers.GetAuth(configPathF)
 	if err != nil {
 		return fmt.Errorf("failed to load config file, reason: %v", err)
 	}

main.go

@@ -49,7 +49,7 @@ var Commands = map[string]commandInfo{
 func main() {
 
 	log.SetLevel(log.WarnLevel)
-	command, args := ParseArgs()
+	command, args, configPath := ParseArgs()
 
 	var err error
 
@@ -61,15 +61,15 @@ func main() {
 	case "decrypt":
 		err = decrypt.Decrypt(args)
 	case "upload":
-		err = upload.Upload(args)
+		err = upload.Upload(args, configPath)
 	case "list":
-		err = list.List(args)
+		err = list.List(args, configPath)
 	case "htsget":
-		err = htsget.Htsget(args)
+		err = htsget.Htsget(args, configPath)
 	case "login":
 		err = login.NewLogin(args)
 	case "download":
-		err = download.Download(args)
+		err = download.Download(args, configPath)
 	case "version":
 		err = version.Version(Version)
 	default:
@@ -84,7 +84,8 @@ func main() {
 
 // Parses the command line arguments into a command, and keep the rest
 // of the arguments for the subcommand.
-func ParseArgs() (string, []string) {
+func ParseArgs() (string, []string, string) {
+	var configPath string
 	// Print usage if no arguments are provided.
 	if len(os.Args) < 2 {
 		_ = Help("help")
@@ -98,7 +99,18 @@ func ParseArgs() (string, []string) {
 			os.Exit(0)
 		}
 
-		return "version", os.Args
+		return "version", os.Args, ""
+	}
+
+	// If config comes before the command, we remove it from the
+	// arguments and set the global config path.
+	if len(os.Args) > 1 && (os.Args[1] == "--config" || os.Args[1] == "-config") {
+		if len(os.Args) < 3 {
+			fmt.Fprintf(os.Stderr, "Error: --config requires an argument\n")
+			os.Exit(1)
+		}
+		configPath = os.Args[2]
+		os.Args = append(os.Args[:1], os.Args[3:]...)
 	}
 
 	// Extract the command from the 1st argument, then remove it
@@ -130,7 +142,7 @@ func ParseArgs() (string, []string) {
 	// The "list" command can have no arguments since it can use the
 	// config from login so we immediately return in that case.
 	if command == "list" {
-		return command, os.Args
+		return command, os.Args, configPath
 	}
 
 	// If no arguments are provided to the subcommand, it's not
@@ -141,7 +153,7 @@ func ParseArgs() (string, []string) {
 		os.Exit(1)
 	}
 
-	return command, os.Args
+	return command, os.Args, configPath
 }
 
 // Prints the main usage string, and the global help or command help

upload/upload.go

@@ -256,7 +256,7 @@ func createFilePaths(dirPath string) ([]string, []string, error) {
 
 // Upload function uploads files to the s3 bucket. Input can be files or
 // directories to be uploaded recursively
-func Upload(args []string) error {
+func Upload(args []string, configPathF string) error {
 	var files []string
 	var outFiles []string
 	*pubKeyPath = ""
@@ -267,6 +267,9 @@ func Upload(args []string) error {
 	if err != nil {
 		return fmt.Errorf("failed parsing arguments, reason: %v", err)
 	}
+	if configPathF == "" {
+		configPathF = *configPath
+	}
 
 	// Dereference the pointer to a string
 	var targetDirString string
@@ -288,7 +291,7 @@ func Upload(args []string) error {
 	}
 
 	// Get the configuration file or the .sda-cli-session
-	config, err := helpers.GetAuth(*configPath)
+	config, err := helpers.GetAuth(configPathF)
 	if err != nil {
 		return err
 	}