undo *cwl.File vs cwl.File

cmd/cwl/run.go

@@ -314,7 +314,6 @@ func (r *runner) runWorkflow(wf *cwl.Workflow, vals cwl.Values) (cwl.Values, err
         stepvals[in.ID] = link.value()
       }
 
-      // TODO failing because of the cwl.File vs *cwl.File mixup
       debug("STEP VALS", stepvals)
       outvals, err := r.runDoc(step.Run, stepvals)
       if err != nil {

process/fs.go

@@ -13,10 +13,10 @@ import (
 var ErrFileNotFound = errors.New("file not found")
 
 type Filesystem interface {
-	Create(path, contents string) (*cwl.File, error)
-	Info(loc string) (*cwl.File, error)
+	Create(path, contents string) (cwl.File, error)
+	Info(loc string) (cwl.File, error)
 	Contents(loc string) (string, error)
-	Glob(pattern string) ([]*cwl.File, error)
+	Glob(pattern string) ([]cwl.File, error)
 }
 
 const MaxContentsBytes = 64 * units.Kilobyte
@@ -25,7 +25,9 @@ const MaxContentsBytes = 64 * units.Kilobyte
 // such as dirname, checksum, size, etc. If f.Contents is given, the
 // file will be created via fs.Create(). if `loadContents` is true,
 // the file contents will be loaded via fs.Contents().
-func (process *Process) resolveFile(f cwl.File, loadContents bool) (*cwl.File, error) {
+func (process *Process) resolveFile(f cwl.File, loadContents bool) (cwl.File, error) {
+	// TODO revisit pointer to File
+	var x cwl.File
 
 	// http://www.commonwl.org/v1.0/CommandLineTool.html#File
 	// "As a special case, if the path field is provided but the location field is not,
@@ -37,16 +39,15 @@ func (process *Process) resolveFile(f cwl.File, loadContents bool) (*cwl.File, e
 	}
 
 	if f.Location == "" && f.Contents == "" {
-		return nil, errf("location and contents are empty")
+		return x, errf("location and contents are empty")
 	}
 
 	// If both location and contents are set, one will get overwritten.
 	// Can't know which one the caller intended, so fail instead.
 	if f.Location != "" && f.Contents != "" {
-		return nil, errf("location and contents are both non-empty")
+		return x, errf("location and contents are both non-empty")
 	}
 
-	var x *cwl.File
 	var err error
 
 	if f.Contents != "" {
@@ -59,26 +60,26 @@ func (process *Process) resolveFile(f cwl.File, loadContents bool) (*cwl.File, e
 		if path == "" {
 			id, err := uuid.NewRandom()
 			if err != nil {
-				return nil, errf("generating a random name for a file literal: %s", err)
+				return x, errf("generating a random name for a file literal: %s", err)
 			}
 			path = id.String()
 		}
 
 		x, err = process.fs.Create(path, f.Contents)
 		if err != nil {
-			return nil, errf("creating file from inline content: %s", err)
+			return x, errf("creating file from inline content: %s", err)
 		}
 
 	} else {
 		x, err = process.fs.Info(f.Location)
 		if err != nil {
-			return nil, errf("getting file info for %q: %s", f.Location, err)
+			return x, errf("getting file info for %q: %s", f.Location, err)
 		}
 
 		if loadContents {
 			f.Contents, err = process.fs.Contents(f.Location)
 			if err != nil {
-				return nil, errf("loading file contents: %s", err)
+				return x, errf("loading file contents: %s", err)
 			}
 		}
 	}
@@ -103,10 +104,10 @@ func (process *Process) resolveFile(f cwl.File, loadContents bool) (*cwl.File, e
 	f.Nameroot, f.Nameext = splitname(f.Basename)
 	f.Dirname = filepath.Dir(f.Path)
 
-	return &f, nil
+	return f, nil
 }
 
-func (process *Process) resolveSecondaryFiles(file *cwl.File, x cwl.Expression) error {
+func (process *Process) resolveSecondaryFiles(file cwl.File, x cwl.Expression) error {
 
 	// cwl spec:
 	// "If the value is an expression, the value of self in the expression

process/fs/local/local.go

@@ -22,8 +22,8 @@ func NewLocal(workdir string) *Local {
 	return &Local{workdir, false}
 }
 
-func (l *Local) Glob(pattern string) ([]*cwl.File, error) {
-	var out []*cwl.File
+func (l *Local) Glob(pattern string) ([]cwl.File, error) {
+	var out []cwl.File
 
 	pattern = filepath.Join(l.workdir, pattern)
 
@@ -43,64 +43,66 @@ func (l *Local) Glob(pattern string) ([]*cwl.File, error) {
 	return out, nil
 }
 
-func (l *Local) Create(path, contents string) (*cwl.File, error) {
+func (l *Local) Create(path, contents string) (cwl.File, error) {
+  var x cwl.File
 	if path == "" {
-		return nil, errf("can't create file with empty path")
+		return x, errf("can't create file with empty path")
 	}
 
 	b := []byte(contents)
 	size := int64(len(b))
 	if units.MetricBytes(size) > process.MaxContentsBytes {
-		return nil, errf("contents is max allowed size (%s)", process.MaxContentsBytes)
+		return x, errf("contents is max allowed size (%s)", process.MaxContentsBytes)
 	}
 
 	loc := filepath.Join(l.workdir, path)
 	abs, err := filepath.Abs(loc)
 	if err != nil {
-		return nil, errf("getting absolute path for %s: %s", loc, err)
+		return x, errf("getting absolute path for %s: %s", loc, err)
 	}
 
-	return &cwl.File{
+	return cwl.File{
 		Location: abs,
 		Path:     path,
 		Checksum: "sha1$" + fmt.Sprintf("%x", sha1.Sum(b)),
 		Size:     size,
 	}, nil
 }
 
-func (l *Local) Info(loc string) (*cwl.File, error) {
+func (l *Local) Info(loc string) (cwl.File, error) {
+  var x cwl.File
 	if !filepath.IsAbs(loc) {
 		loc = filepath.Join(l.workdir, loc)
 	}
 
 	st, err := os.Stat(loc)
 	if os.IsNotExist(err) {
-		return nil, process.ErrFileNotFound
+		return x, process.ErrFileNotFound
 	}
 	if err != nil {
-		return nil, err
+		return x, err
 	}
 
 	// TODO make this work with directories
 	if st.IsDir() {
-		return nil, errf("can't call Info() on a directory: %s", loc)
+		return x, errf("can't call Info() on a directory: %s", loc)
 	}
 
 	abs, err := filepath.Abs(loc)
 	if err != nil {
-		return nil, errf("getting absolute path for %s: %s", loc, err)
+		return x, errf("getting absolute path for %s: %s", loc, err)
 	}
 
 	checksum := ""
 	if l.CalcChecksum {
 		b, err := ioutil.ReadFile(loc)
 		if err != nil {
-			return nil, errf("calculating checksum for %s: %s", loc, err)
+			return x, errf("calculating checksum for %s: %s", loc, err)
 		}
 		checksum = "sha1$" + fmt.Sprintf("%x", sha1.Sum(b))
 	}
 
-	return &cwl.File{
+	return cwl.File{
 		Location: abs,
 		Path:     abs,
 		Checksum: checksum,

process/inputs.go

@@ -205,7 +205,7 @@ Loop:
 			}
 
 			return []*Binding{
-				{clb, z, *f, key, nil, name},
+				{clb, z, f, key, nil, name},
 			}, nil
 
 		case cwl.DirectoryType:

process/outputs.go

@@ -141,7 +141,7 @@ Loop:
 			}
 		case cwl.FileType:
 			switch y := val.(type) {
-			case []*cwl.File:
+			case []cwl.File:
 				if len(y) != 1 {
 					continue Loop
 				}
@@ -154,9 +154,6 @@ Loop:
 				}
 				return f, nil
 
-				// TODO returning both pointer and non-pointer
-			case *cwl.File:
-				return y, nil
 			case cwl.File:
 				return y, nil
 			default:
@@ -197,10 +194,10 @@ Loop:
 
 // matchFiles executes the list of glob patterns, returning a list of matched files.
 // matchFiles must return a non-nil list on success, even if no files are matched.
-func (process *Process) matchFiles(fs Filesystem, globs []string, loadContents bool) ([]*cwl.File, error) {
+func (process *Process) matchFiles(fs Filesystem, globs []string, loadContents bool) ([]cwl.File, error) {
 	// it's important this slice isn't nil, because the outputEval field
 	// expects it to be non-null during expression evaluation.
-	files := []*cwl.File{}
+	files := []cwl.File{}
 
 	// resolve all the globs into file objects.
 	for _, pattern := range globs {