Merge pull request #296 from metrumresearchgroup/windows-fixups

Windows fixes

cmd/init.go

@@ -7,6 +7,7 @@ import (
 	"os"
 	"path/filepath"
 	"regexp"
+	"runtime"
 	"strings"
 
 	"github.com/metrumresearchgroup/bbi/configlib"
@@ -28,6 +29,13 @@ func initializer(cmd *cobra.Command, _ []string) error {
 		return fmt.Errorf("get dir string: %w", err)
 	}
 
+	var find_nm func(string) (string, error)
+	if runtime.GOOS == "windows" {
+		find_nm = findNonMemBinaryWindows
+	} else {
+		find_nm = findNonMemBinary
+	}
+
 	for _, l := range dir {
 		var files []os.FileInfo
 		// For each directory underneath the dir provided. Let's see if it's nonmemmy
@@ -51,7 +59,7 @@ func initializer(cmd *cobra.Command, _ []string) error {
 
 		for _, v := range locations {
 			var nm string
-			nm, err = findNonMemBinary(v)
+			nm, err = find_nm(v)
 			if err != nil {
 				log.Println(err)
 
@@ -133,6 +141,12 @@ func isPathNonMemmy(path string) bool {
 		return false
 	}
 
+	// That rest of this function (checking for an executable bit in
+	// file mode bits) isn't relevant for Windows.
+	if runtime.GOOS == "windows" {
+		return true
+	}
+
 	// Are any of them executable?
 	fails := 0
 
@@ -188,6 +202,35 @@ func findNonMemBinary(path string) (string, error) {
 	return "", errors.New("No nonmem binary could be located in the given path. Please check again or try another directory")
 }
 
+// findNonMemBinaryWindows is a Windows-specific variant of
+// findNonMemBinary.  The key differences are that 1) it expects
+// ".bat" at the end of the binary and 2) it doesn't expect an
+// executable bit to be set.
+func findNonMemBinaryWindows(path string) (string, error) {
+	rdir := filepath.Join(path, "run")
+	fd, err := os.Open(rdir)
+	if err != nil {
+		return "", err
+	}
+	defer fd.Close()
+
+	re := regexp.MustCompile(`^nmfe[0-9]{2}\.bat$`)
+	files, err := fd.Readdirnames(-1)
+	if err != nil {
+		return "", err
+	}
+
+	for _, fname := range files {
+		// Follow findNonMemBinary() and take the first match (rather
+		// than, e.g., returning an error if multiple files match).
+		if re.MatchString(fname) {
+			return fname, nil
+		}
+	}
+
+	return "", fmt.Errorf("nmfe .bat file not found in %s", rdir)
+}
+
 func hasNMQual(path string) bool {
 	fs := afero.NewOsFs()
 

cmd/init_test.go

@@ -0,0 +1,35 @@
+package cmd
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/metrumresearchgroup/wrapt"
+)
+
+func TestFindNonMemBinaryWindows(tt *testing.T) {
+	t := wrapt.WrapT(tt)
+	dir := t.TempDir()
+	rdir := filepath.Join(dir, "run")
+	if err := os.Mkdir(rdir, 0777); err != nil {
+		t.Fatal(err)
+	}
+
+	foo := filepath.Join(rdir, "foo.bat")
+	if err := os.WriteFile(foo, []byte(""), 0666); err != nil {
+		t.Fatal(err)
+	}
+
+	_, err := findNonMemBinaryWindows(dir)
+	t.R.Contains(err.Error(), ".bat file not found")
+
+	nmfe := filepath.Join(rdir, "nmfe23.bat")
+	if err = os.WriteFile(nmfe, []byte(""), 0666); err != nil {
+		t.Fatal(err)
+	}
+
+	binary, err := findNonMemBinaryWindows(dir)
+	t.R.NoError(err)
+	t.R.Equal(binary, "nmfe23.bat")
+}

cmd/local.go

@@ -443,7 +443,16 @@ func executeLocalJob(model *NonMemModel) turnstile.ConcurrentError {
 
 	log.Debugf("Script location is pegged at %s", scriptLocation)
 
-	command := exec.Command(scriptLocation)
+	bash, err := exec.LookPath("bash")
+	if err != nil {
+		return turnstile.ConcurrentError{
+			Error:         err,
+			RunIdentifier: model.FileName,
+			Notes:         "bash is required to run bbi. Please install bash and then try running this again.",
+		}
+	}
+
+	command := exec.Command(bash, scriptLocation)
 	command.Dir = model.OutputDir
 	command.Env = os.Environ() // Take in OS Environment
 

cmd/run.go

@@ -287,8 +287,13 @@ func ExecutePostWorkDirectivesWithEnvironment(worker PostWorkExecutor) (string,
 		return "", err
 	}
 
+	bash, err := exec.LookPath("bash")
+	if err != nil {
+		return "", err
+	}
+
 	// Needs to be the processed value, not the config template.
-	cmd := exec.Command(filepath.Join(worker.GetWorkingPath(), "post_processing.sh"))
+	cmd := exec.Command(bash, filepath.Join(worker.GetWorkingPath(), "post_processing.sh"))
 
 	// Set the environment for the binary.
 	cmd.Env = environment