[ARVADOS] updated: 1.1.2-138-gc8891a5

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py  | 10 +++++++---
 sdk/cwl/arvados_cwl/arvtool.py   |  2 +-
 services/crunch-run/crunchrun.go | 30 +++++++++++++++++++-----------
 3 files changed, 27 insertions(+), 15 deletions(-)

       via  c8891a5eeec540404c7aff02a200fd95f6dbe64b (commit)
      from  3e51fd869e600fd3d60e892346896fd9ce3d8c9c (commit)

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commit c8891a5eeec540404c7aff02a200fd95f6dbe64b
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Mon Jan 29 15:58:46 2018 -0500

    12764: Improve error handling around staging writable files
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index af6ab33..a55db8d 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -227,9 +227,13 @@ class ArvCwlRunner(object):
             if obj.get("writable") and self.work_api != "containers":
                 raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported with --api=jobs")
             if obj.get("class") == "DockerRequirement":
-                if obj.get("dockerOutputDirectory") and self.work_api != "containers":
-                    raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError(
-                        "Option 'dockerOutputDirectory' of DockerRequirement not supported with --api=jobs.")
+                if obj.get("dockerOutputDirectory"):
+                    if self.work_api != "containers":
+                        raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError(
+                            "Option 'dockerOutputDirectory' of DockerRequirement not supported with --api=jobs.")
+                    if not obj.get("dockerOutputDirectory").startswith('/'):
+                        raise SourceLine(obj, "dockerOutputDirectory", validate.ValidationException).makeError(
+                            "Option 'dockerOutputDirectory' must be an absolute path.")
             for v in obj.itervalues():
                 self.check_features(v)
         elif isinstance(obj, list):
diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 52f7d8a..81faff4 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -37,7 +37,7 @@ class ArvadosCommandTool(CommandLineTool):
     def job(self, joborder, output_callback, **kwargs):
         if self.work_api == "containers":
             dockerReq, is_req = self.get_requirement("DockerRequirement")
-            if dockerReq.get("dockerOutputDirectory") and dockerReq.get("dockerOutputDirectory").startswith('/'):
+            if dockerReq and dockerReq.get("dockerOutputDirectory"):
                 kwargs["outdir"] = dockerReq.get("dockerOutputDirectory")
                 kwargs["docker_outdir"] = dockerReq.get("dockerOutputDirectory")
             else:
diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go
index 852d5a2..1f94973 100644
--- a/services/crunch-run/crunchrun.go
+++ b/services/crunch-run/crunchrun.go
@@ -577,20 +577,28 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
 
 	for _, cp := range copyFiles {
 		dir, err := os.Stat(cp.src)
-		if err == nil {
-			if dir.IsDir() {
-				err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
-					if walkinfo.Mode().IsRegular() {
-						return copyfile(walkpath, path.Join(cp.bind, walkpath[len(cp.src):]))
-					}
+		if err != nil {
+			return fmt.Errorf("While staging writable file from %q to %q: %v", cp.src, cp.bind, err)
+		}
+		if dir.IsDir() {
+			err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
+				if walkerr != nil {
+					return walkerr;
+				}
+				if walkinfo.Mode().IsRegular() {
+					return copyfile(walkpath, path.Join(cp.bind, walkpath[len(cp.src):]))
+				} else if walkinfo.Mode().IsDir() {
+					// will be visited by Walk()
 					return nil
-				})
-			} else {
-				err = copyfile(cp.src, cp.bind)
-			}
+				} else {
+					return fmt.Errorf("Source %q is not a regular file or directory", cp.src)
+				}
+			})
+		} else {
+			err = copyfile(cp.src, cp.bind)
 		}
 		if err != nil {
-			return fmt.Errorf("While staging writable files: %v", err)
+			return fmt.Errorf("While staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 		}
 	}
 

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