-
Notifications
You must be signed in to change notification settings - Fork 2
/
root.go
75 lines (63 loc) · 2.08 KB
/
root.go
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
package cmd
import (
"errors"
"fmt"
"log"
"os"
"path"
"github.com/chanzuckerberg/czid-cli/cmd/consensusGenome"
"github.com/chanzuckerberg/czid-cli/cmd/generateMetadataTemplate"
"github.com/chanzuckerberg/czid-cli/cmd/metagenomics"
"github.com/chanzuckerberg/czid-cli/pkg/util"
"github.com/spf13/cobra"
"github.com/spf13/viper"
)
var cfgFile string
// RootCmd represents the base command when called without any subcommands
var RootCmd = &cobra.Command{
Use: "czid",
Short: "A CLI for uploading samples to Chan Zuckerberg ID",
}
func init() {
RootCmd.AddCommand(metagenomics.MetagenomicsCmd)
RootCmd.AddCommand(consensusGenome.ConsensusGenomeCmd)
RootCmd.AddCommand(generateMetadataTemplate.GenerateMetadataTemplateCmd)
}
// Execute adds all child commands to the root command and sets flags appropriately.
// This is called by main.main(). It only needs to happen once to the rootCmd.
func Execute() {
if err := RootCmd.Execute(); err != nil {
fmt.Println(err)
os.Exit(1)
}
}
func init() {
cobra.OnInitialize(initConfig)
RootCmd.PersistentFlags().StringVar(&cfgFile, "config", "", "config file")
RootCmd.PersistentFlags().BoolP("verbose", "v", false, "Print verbose logs")
}
// initConfig reads in config file and ENV variables if set.
func initConfig() {
if cfgFile != "" {
// Use config file from the flag.
viper.SetConfigFile(cfgFile)
} else {
configDir, err := util.GetConfigDir()
if err != nil {
log.Fatal(err)
}
viper.SetConfigFile(path.Join(configDir, "config.yaml"))
}
// Check if verbose flag is set
verbose, _ := RootCmd.Flags().GetBool("verbose")
viper.SetEnvPrefix("czid_cli")
viper.AutomaticEnv() // read in environment variables that match
// If a config file is found, read it in.
if err := viper.ReadInConfig(); err != nil {
if !errors.Is(err, os.ErrNotExist) {
log.Fatalf("Error reading config file: %s\n", err.Error())
} else if verbose {
fmt.Println("Config file not found. Run the command with '--config' to explicitly pass in a config.yaml file. Or set environment variables with the prefix CZID_CLI_* (eg CZID_CLI_SECRET)")
}
}
}