[ARVADOS] created: 1.1.2-47-g6fe6695

[Git user]

        at  6fe66955fb53dde27d9677d31fdb137913b2b850 (commit)


commit 6fe66955fb53dde27d9677d31fdb137913b2b850
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Jan 10 11:58:53 2018 -0500

    12934: crunch-run creates .keep file in empty directories
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go
index e5e0ea0..59fdd00 100644
--- a/services/crunch-run/crunchrun.go
+++ b/services/crunch-run/crunchrun.go
@@ -1051,6 +1051,21 @@ func (runner *ContainerRunner) UploadOutputFile(
 	followed int) (manifestText string, err error) {
 
 	if info.Mode().IsDir() {
+		// if empty, need to create a .keep file
+		dir, direrr := os.Open(path)
+		if (direrr != nil) {
+			return "", direrr
+		}
+		defer dir.Close()
+		names, eof := dir.Readdirnames(1)
+		if len(names) == 0 && eof == io.EOF {
+			keep, keeperr := os.Create(path+"/.keep")
+			if keeperr != nil {
+				return "", keeperr
+			}
+			keep.Close()
+		}
+
 		return
 	}
 

commit 0dd6cd18de9b20a85c0bbbcd0df4e497743a132d
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Jan 10 10:42:20 2018 -0500

    12934: Sort glob results
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 5e3d685..47749ee 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -110,7 +110,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
         if collection is not None and not rest:
             return [pattern]
         patternsegments = rest.split("/")
-        return self._match(collection, patternsegments, "keep:" + collection.manifest_locator())
+        return sorted(self._match(collection, patternsegments, "keep:" + collection.manifest_locator()))
 
     def open(self, fn, mode):
         collection, rest = self.get_collection(fn)

commit 479aa841b36246aa16e4cf77f78cdb8b93bc8de1
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue Jan 9 21:49:06 2018 -0500

    12934: Bump cwltool and schema salad
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index ae48735..de47098 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -41,8 +41,8 @@ setup(name='arvados-cwl-runner',
       # Note that arvados/build/run-build-packages.sh looks at this
       # file to determine what version of cwltool and schema-salad to build.
       install_requires=[
-          'cwltool==1.0.20170928192020',
-          'schema-salad==2.6.20171116190026',
+          'cwltool==1.0.20180111185617',
+          'schema-salad==2.6.20171201034858',
           'typing==3.5.3.0',
           'ruamel.yaml==0.13.7',
           'arvados-python-client>=0.1.20170526013812',

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