12764: Pass one cwl test

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go
index 5437e3653aa8939fda4bb453b173630f8ec40c36..852d5a27b168270d46cad855755cb5019a732f72 100644 (file)
--- a/services/crunch-run/crunchrun.go
+++ b/services/crunch-run/crunchrun.go
@@ -342,7 +342,7 @@ func copyfile(src string, dst string) (err error) {
        if err != nil {
                return
        }
-       _, err = io.Copy(srcfile, dstfile)
+       _, err = io.Copy(dstfile, srcfile)
        if err != nil {
                return
        }
@@ -1135,7 +1135,7 @@ func (runner *ContainerRunner) UploadOutputFile(
        // go through mounts and try reverse map to collection reference
        for _, bind := range binds {
                mnt := runner.Container.Mounts[bind]
-               if tgt == bind || strings.HasPrefix(tgt, bind+"/") {
+               if (tgt == bind || strings.HasPrefix(tgt, bind+"/")) && !mnt.Writable {
                        // get path relative to bind
                        targetSuffix := tgt[len(bind):]
 
@@ -1274,7 +1274,7 @@ func (runner *ContainerRunner) CaptureOutput() error {
                        continue
                }
 
-               if mnt.ExcludeFromOutput == true {
+               if mnt.ExcludeFromOutput == true || mnt.Writable {
                        continue
                }