Merge pull request #206 from metrumresearchgroup/fmt/proj

fmt: go fmt project

cmd/covcor.go

@@ -15,9 +15,9 @@
 package cmd
 
 import (
+	parser "bbi/parsers/nmparser"
 	"encoding/json"
 	"fmt"
-	parser "bbi/parsers/nmparser"
 	log "github.com/sirupsen/logrus"
 
 	"github.com/spf13/cobra"
@@ -28,12 +28,13 @@ const covcorLongDescription string = `load .cov and .cor output from model(s), f
 bbi nonmem covcor run001/run001
 bbi nonmem covcor run001/run001.cov
  `
+
 // runCmd represents the run command
 var covcorCmd = &cobra.Command{
 	Use:   "covcor",
 	Short: "load .cov and .cor output from a model run",
-	Long: covcorLongDescription,
-	Run: covcor,
+	Long:  covcorLongDescription,
+	Run:   covcor,
 }
 
 func covcor(cmd *cobra.Command, args []string) {
@@ -52,4 +53,4 @@ func covcor(cmd *cobra.Command, args []string) {
 }
 func init() {
 	nonmemCmd.AddCommand(covcorCmd)
-}
+}

cmd/init.go

@@ -7,8 +7,8 @@ import (
 	"regexp"
 	"strings"
 
-	"github.com/ghodss/yaml"
 	"bbi/configlib"
+	"github.com/ghodss/yaml"
 
 	"github.com/spf13/afero"
 	"github.com/spf13/cobra"

cmd/local.go

@@ -1,11 +1,11 @@
 package cmd
 
 import (
+	"bbi/configlib"
 	"crypto/md5"
 	"encoding/json"
 	"errors"
 	"fmt"
-	"bbi/configlib"
 	log "github.com/sirupsen/logrus"
 	"io"
 	"os/exec"

cmd/nonmem.go

@@ -173,8 +173,8 @@ var nonmemLongDescription string = fmt.Sprintf("\n%s\n\n%s\n\n%s\n", runLongDesc
 var nonmemCmd = &cobra.Command{
 	Use:   "nonmem",
 	Short: "nonmem a (set of) models locally or on the grid",
-	Long: nonmemLongDescription,
-	Run: nonmem,
+	Long:  nonmemLongDescription,
+	Run:   nonmem,
 }
 
 func nonmem(cmd *cobra.Command, args []string) {
@@ -272,7 +272,6 @@ func copyFileToDestination(l *NonMemModel, modifyPath bool) error {
 
 		//We'll use stats for setting the mode of the target file to make sure perms are the same
 
-
 		for k, line := range sourceLines {
 			if strings.Contains(line, "$DATA") {
 				sourceLines[k] = parser.AddPathLevelToData(line)
@@ -725,7 +724,7 @@ func NewNonMemModel(modelname string, config configlib.Config) (NonMemModel, err
 	lm.OriginalModel = lm.Model
 
 	f, e := utils.FileAndExt(lm.Model)
-	lm.FileName  = f
+	lm.FileName = f
 	lm.Extension = strings.TrimPrefix(e, ".")
 
 	//Get the raw path of the original by stripping the actual file from it

cmd/nonmem_test.go

@@ -7,8 +7,8 @@ import (
 	"reflect"
 	"testing"
 
-	"github.com/google/uuid"
 	"bbi/configlib"
+	"github.com/google/uuid"
 	"github.com/spf13/afero"
 )
 
@@ -79,22 +79,22 @@ func Test_processNMFEOptions(t *testing.T) {
 			name: "Normal Operation",
 			args: args{
 				config: configlib.Config{
-					NMVersion:     "",
-					Overwrite:     false,
-					CleanLvl:      0,
-					CopyLvl:       0,
-					Git:           false,
-					BbiBinary:     "",
-					SaveConfig:    false,
-					OutputDir:     "",
-					Threads:       0,
-					Debug:         false,
-					Local:         configlib.LocalDetail{},
-					Nonmem:        nil,
-					Delay:         0,
-					NMQual:        false,
-					JSON:          false,
-					Logfile:       "",
+					NMVersion:  "",
+					Overwrite:  false,
+					CleanLvl:   0,
+					CopyLvl:    0,
+					Git:        false,
+					BbiBinary:  "",
+					SaveConfig: false,
+					OutputDir:  "",
+					Threads:    0,
+					Debug:      false,
+					Local:      configlib.LocalDetail{},
+					Nonmem:     nil,
+					Delay:      0,
+					NMQual:     false,
+					JSON:       false,
+					Logfile:    "",
 					NMFEOptions: configlib.NMFEOptions{
 						LicenseFile: "/tmp/nonmem.lic",
 						PRSame:      false,
@@ -116,22 +116,22 @@ func Test_processNMFEOptions(t *testing.T) {
 			name: "All booleans, no text",
 			args: args{
 				config: configlib.Config{
-					NMVersion:     "",
-					Overwrite:     false,
-					CleanLvl:      0,
-					CopyLvl:       0,
-					Git:           false,
-					BbiBinary:     "",
-					SaveConfig:    false,
-					OutputDir:     "",
-					Threads:       0,
-					Debug:         false,
-					Local:         configlib.LocalDetail{},
-					Nonmem:        nil,
-					Delay:         0,
-					NMQual:        false,
-					JSON:          false,
-					Logfile:       "",
+					NMVersion:  "",
+					Overwrite:  false,
+					CleanLvl:   0,
+					CopyLvl:    0,
+					Git:        false,
+					BbiBinary:  "",
+					SaveConfig: false,
+					OutputDir:  "",
+					Threads:    0,
+					Debug:      false,
+					Local:      configlib.LocalDetail{},
+					Nonmem:     nil,
+					Delay:      0,
+					NMQual:     false,
+					JSON:       false,
+					Logfile:    "",
 					NMFEOptions: configlib.NMFEOptions{
 						LicenseFile: "",
 						PRSame:      true,

cmd/root.go

@@ -15,21 +15,21 @@
 package cmd
 
 import (
+	"bbi/configlib"
 	"fmt"
 	"github.com/metrumresearchgroup/turnstile"
 	log "github.com/sirupsen/logrus"
 	"github.com/spf13/afero"
+	"github.com/spf13/cobra"
+	flag "github.com/spf13/pflag"
+	"github.com/spf13/viper"
 	"io"
 	"math/rand"
 	"os"
 	"path"
 	"path/filepath"
 	"sync"
 	"time"
-	"bbi/configlib"
-	"github.com/spf13/cobra"
-	flag "github.com/spf13/pflag"
-	"github.com/spf13/viper"
 )
 
 // VERSION is the current bbi version

cmd/run.go

@@ -1,8 +1,8 @@
 package cmd
 
 import (
-	"bytes"
 	"bbi/configlib"
+	"bytes"
 	"github.com/metrumresearchgroup/turnstile"
 	log "github.com/sirupsen/logrus"
 	"github.com/spf13/cobra"
@@ -242,7 +242,7 @@ func ExecutePostWorkDirectivesWithEnvironment(worker PostWorkExecutor) (string,
 
 	environment, err := PostExecutionEnvironment(postworkConfig, postWorkEnv)
 
-	environment = append(environment,os.Environ()...)
+	environment = append(environment, os.Environ()...)
 
 	log.WithFields(log.Fields{
 		"environment": environment,

cmd/sge.go

@@ -1,9 +1,9 @@
 package cmd
 
 import (
+	"bbi/utils"
 	"bytes"
 	"errors"
-	"bbi/utils"
 	log "github.com/sirupsen/logrus"
 	"os/exec"
 	"path"
@@ -288,7 +288,7 @@ func executeSGEJob(model *NonMemModel) turnstile.ConcurrentError {
 		}...)
 	}
 
-	qsubArguments = append(qsubArguments, filepath.Join(model.OutputDir,scriptName))
+	qsubArguments = append(qsubArguments, filepath.Join(model.OutputDir, scriptName))
 
 	if err != nil {
 		return newConcurrentError(model.Model, "Could not locate qsub binary in path", err)
@@ -305,7 +305,7 @@ func executeSGEJob(model *NonMemModel) turnstile.ConcurrentError {
 
 	if len(additionalEnvs) > 0 {
 		log.Debugf("Additional post work envs were provided. Total of %d", len(additionalEnvs))
-		command.Env = append(command.Env,additionalEnvs...)
+		command.Env = append(command.Env, additionalEnvs...)
 	}
 
 	output, err := command.CombinedOutput()

cmd/summary.go

@@ -15,9 +15,9 @@
 package cmd
 
 import (
+	parser "bbi/parsers/nmparser"
 	"encoding/json"
 	"fmt"
-	parser "bbi/parsers/nmparser"
 	log "github.com/sirupsen/logrus"
 	"os"
 	"runtime"
@@ -33,6 +33,7 @@ var (
 	noShk       bool
 	extFile     string
 )
+
 const summaryLongDescription string = `summarize model(s), for example: 
 bbi nonmem summary run001/run001
 bbi nonmem summary run001/run001.lst
@@ -43,8 +44,8 @@ bbi nonmem summary run001/run001.res
 var summaryCmd = &cobra.Command{
 	Use:   "summary",
 	Short: "summarize the output of model(s)",
-	Long: summaryLongDescription,
-	Run: summary,
+	Long:  summaryLongDescription,
+	Run:   summary,
 }
 
 type jsonResults struct {
@@ -57,7 +58,7 @@ func summary(cmd *cobra.Command, args []string) {
 		viper.Debug()
 	}
 	if len(args) == 1 {
-		results, err := parser.GetModelOutput(args[0], parser.NewModelOutputFile(extFile, noExt), !noGrd, !noShk, )
+		results, err := parser.GetModelOutput(args[0], parser.NewModelOutputFile(extFile, noExt), !noGrd, !noShk)
 		if err != nil {
 			log.Fatal(err)
 		}
@@ -102,7 +103,7 @@ func summary(cmd *cobra.Command, args []string) {
 	for w := 1; w <= workers; w++ {
 		go func(w int, modIndex <-chan int, results chan<- modelResult) {
 			for i := range modIndex {
-				r, err := parser.GetModelOutput(args[i], parser.NewModelOutputFile(extFile, noExt), !noGrd, !noShk, )
+				r, err := parser.GetModelOutput(args[i], parser.NewModelOutputFile(extFile, noExt), !noGrd, !noShk)
 				if err != nil {
 					results <- modelResult{
 						Index:   i,
@@ -142,12 +143,11 @@ func summary(cmd *cobra.Command, args []string) {
 		return
 	}
 
-
 	// not json lets print all successful models first then any errors
 	for i, res := range modelResults.Results {
 		res.Summary()
 		// add some spacing between models
-		if i != len(modelResults.Results) -1 {
+		if i != len(modelResults.Results)-1 {
 			fmt.Println("")
 			fmt.Println("")
 		}

configlib/config.go

@@ -36,7 +36,7 @@ type Config struct {
 	Parafile           string                  `mapstructure:"parafile" yaml:"parafile" json:"parafile,omitempty"`
 	PostWorkExecutable string                  `mapstructure:"post_work_executable" yaml:"post_work_executable" json:"post_work_executable,omitempty"`
 	postWorkExecEnvs   []string                `mapstructure:"additional_post_work_envs" yaml:"additional_post_work_envs" json:"additional_post_work_envs,omitempty"`
-	GridNamePrefix  string                     `mapstructure:"grid_name_prefix" yaml:"grid_name_prefix" json:"grid_name_prefix,omitempty"`
+	GridNamePrefix     string                  `mapstructure:"grid_name_prefix" yaml:"grid_name_prefix" json:"grid_name_prefix,omitempty"`
 }
 
 func (c *Config) GetPostWorkExecEnvs() []string {