#10 add environment variables and command line arguments to DB tool

cmd/mb3dbtool/main.go

@@ -1,12 +1,66 @@
 package main
 
-import "github.com/MassBank/MassBank3/pkg/database"
+import (
+	"errors"
+	"flag"
+	"github.com/MassBank/MassBank3/pkg/database"
+	"os"
+	"strconv"
+)
+
+type config struct {
+	database.DBConfig
+	gitRepo string
+	dataDir string
+}
 
 func main() {
-	database, err := database.NewMongoDB()
+	var userConfig = getConfig()
+	var db database.MB3Database
+	var err error
+	db, err = database.NewMongoDB(userConfig.DBConfig)
+	if err != nil {
+		panic(err)
+	}
+	err = db.Connect()
 	if err != nil {
 		panic(err)
 	}
-	database.Connect()
+}
+
+func getEnv(name string, fallback string) string {
+	if value, ok := os.LookupEnv(name); ok {
+		return value
+	}
+	return fallback
+}
 
+func getConfig() config {
+	var c = config{}
+	c.DbUser = getEnv("DB_USER", "massbank3")
+	c.DbPwd = getEnv("DB_PASSWORD", "massbank3password")
+	c.DbHost = getEnv("DB_HOST", "localhost")
+	c.DbName = getEnv("DB_NAME", "massbank3")
+	c.DbConnStr = getEnv("DB_CONN_STRING", "")
+	c.gitRepo = getEnv("MB_GIT_REPO", "https://github.com/MassBank/MassBank-data.git")
+	c.dataDir = getEnv("MB_DATA_DIRECTORY", "")
+	var dbPortEnv = getEnv("DB_PORT", "27017")
+	dbPort, err := strconv.ParseUint(dbPortEnv, 10, 16)
+	if err != nil {
+		panic(errors.New("Could not read port variable: DB_PORT=" + dbPortEnv))
+	}
+	c.DbPort = uint(dbPort)
+	flag.StringVar(&c.DbUser, "user", c.DbUser, "database user name")
+	flag.StringVar(&c.DbPwd, "pwd", c.DbPwd, "database user password")
+	flag.StringVar(&c.DbHost, "host", c.DbHost, "database host")
+	flag.StringVar(&c.DbName, "db", c.DbName, "database name")
+	flag.UintVar(&c.DbPort, "port", c.DbPort, "database port")
+	flag.StringVar(&c.DbConnStr, "connstr", c.DbConnStr, "database connection string")
+	flag.StringVar(&c.gitRepo, "git", c.gitRepo, "git host")
+	flag.StringVar(&c.dataDir, "dir", c.dataDir, "data directory")
+	flag.Parse()
+	if len(c.gitRepo) > 0 && len(c.dataDir) > 0 {
+		println("Git repo and data directory are set. Using data directory as default and git repo as fallback.")
+	}
+	return c
 }

go.mod

@@ -7,6 +7,7 @@ require github.com/go-chi/chi/v5 v5.0.3
 require (
 	github.com/go-chi/cors v1.2.0
 	go.mongodb.org/mongo-driver v1.11.1
+	golang.org/x/net v0.0.0-20211112202133-69e39bad7dc2
 )
 
 require (

go.sum

@@ -39,6 +39,7 @@ go.mongodb.org/mongo-driver v1.11.1 h1:QP0znIRTuL0jf1oBQoAoM0C6ZJfBK4kx0Uumtv1A7
 go.mongodb.org/mongo-driver v1.11.1/go.mod h1:s7p5vEtfbeR1gYi6pnj3c3/urpbLv2T5Sfd6Rp2HBB8=
 golang.org/x/crypto v0.0.0-20220622213112-05595931fe9d h1:sK3txAijHtOK88l68nt020reeT1ZdKLIYetKl95FzVY=
 golang.org/x/crypto v0.0.0-20220622213112-05595931fe9d/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=
+golang.org/x/net v0.0.0-20211112202133-69e39bad7dc2 h1:CIJ76btIcR3eFI5EgSo6k1qKw9KJexJuRLI9G7Hp5wE=
 golang.org/x/net v0.0.0-20211112202133-69e39bad7dc2/go.mod h1:9nx3DQGgdP8bBQD5qxJ1jj9UTztislL4KSBs9R2vV5Y=
 golang.org/x/sync v0.0.0-20210220032951-036812b2e83c h1:5KslGYwFpkhGh+Q16bwMP3cOontH8FOep7tGV86Y7SQ=
 golang.org/x/sync v0.0.0-20210220032951-036812b2e83c/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=

pkg/database/db_interface.go

@@ -5,6 +5,15 @@ import "github.com/MassBank/MassBank3/pkg/massbank"
 type Filters struct {
 }
 
+type DBConfig struct {
+	DbUser    string
+	DbPwd     string
+	DbHost    string
+	DbName    string
+	DbPort    uint
+	DbConnStr string
+}
+
 type MB3Database interface {
 	Connect() error
 	Disconnect() error

pkg/database/mongodb.go

@@ -50,17 +50,16 @@ func (self *Mb3MongoDB) UpdateRecord(record massbank.Massbank, add bool) error {
 	panic("implement me")
 }
 
-func NewMongoDB() (*Mb3MongoDB, error) {
+func NewMongoDB(config DBConfig) (*Mb3MongoDB, error) {
 	return &Mb3MongoDB{
-		user:     "massbank3",
-		pwd:      "massbank3password",
-		host:     "localhost",
-		dbname:   "massbank3",
-		port:     27017,
+		user:     config.DbUser,
+		pwd:      config.DbPwd,
+		host:     config.DbHost,
+		dbname:   config.DbName,
+		port:     uint16(config.DbPort),
 		database: nil,
 		dirty:    true,
 	}, nil
-
 }
 
 func (self *Mb3MongoDB) SetUser(user string) *Mb3MongoDB {