[ARVADOS] created: 1.1.4-321-g95c01d2

[Git user]

        at  95c01d22571043d7b6405f928538204cf930d453 (commit)


commit 95c01d22571043d7b6405f928538204cf930d453
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date:   Fri Jun 1 18:06:49 2018 +0200

    Add storage classes supper to arvados cwl runner
    
    Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index d509f40..6d4eda4 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -279,7 +279,7 @@ class ArvCwlRunner(object):
                 with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)):
                     self.check_features(v)
 
-    def make_output_collection(self, name, tagsString, outputObj):
+    def make_output_collection(self, name, storage_classes, tagsString, outputObj):
         outputObj = copy.deepcopy(outputObj)
 
         files = []
@@ -330,7 +330,7 @@ class ArvCwlRunner(object):
         with final.open("cwl.output.json", "w") as f:
             json.dump(outputObj, f, sort_keys=True, indent=4, separators=(',',': '))
 
-        final.save_new(name=name, owner_uuid=self.project_uuid, ensure_unique_name=True)
+        final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes, ensure_unique_name=True)
 
         logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(),
                     final.api_response()["name"],
@@ -592,6 +592,7 @@ class ArvCwlRunner(object):
         if self.final_output is None:
             raise WorkflowException("Workflow did not return a result.")
 
+
         if kwargs.get("submit") and isinstance(runnerjob, Runner):
             logger.info("Final output collection %s", runnerjob.final_output)
         else:
@@ -599,7 +600,12 @@ class ArvCwlRunner(object):
                 self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
             if self.output_tags is None:
                 self.output_tags = ""
-            self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.output_tags, self.final_output)
+
+            storage_classes = ["default"]
+            if kwargs.get("storage_classes"):
+                storage_classes = kwargs.get("storage_classes").strip().split(",")
+
+            self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes, self.output_tags, self.final_output)
             self.set_crunch_output()
 
         if kwargs.get("compute_checksum"):
@@ -717,6 +723,8 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     parser.add_argument("--enable-dev", action="store_true",
                         help="Enable loading and running development versions "
                              "of CWL spec.", default=False)
+    parser.add_argument('--storage-classes', 
+                        help="Specify comma separated list of storage classes to be used when saving wortkflow output to Keep.")
 
     parser.add_argument("--intermediate-output-ttl", type=int, metavar="N",
                         help="If N > 0, intermediate output collections will be trashed N seconds after creation.  Default is 0 (don't trash).",
diff --git a/sdk/cwl/tests/test_make_output.py b/sdk/cwl/tests/test_make_output.py
index 806d63a..13b1aff 100644
--- a/sdk/cwl/tests/test_make_output.py
+++ b/sdk/cwl/tests/test_make_output.py
@@ -39,7 +39,7 @@ class TestMakeOutput(unittest.TestCase):
         final.open.return_value = openmock
         openmock.__enter__.return_value = cwlout
 
-        _, runner.final_output_collection = runner.make_output_collection("Test output", "tag0,tag1,tag2", {
+        _, runner.final_output_collection = runner.make_output_collection("Test output", ["default"], "tag0,tag1,tag2", {
             "foo": {
                 "class": "File",
                 "location": "keep:99999999999999999999999999999991+99/foo.txt",
@@ -56,7 +56,7 @@ class TestMakeOutput(unittest.TestCase):
 
         final.copy.assert_has_calls([mock.call('bar.txt', 'baz.txt', overwrite=False, source_collection=readermock)])
         final.copy.assert_has_calls([mock.call('foo.txt', 'foo.txt', overwrite=False, source_collection=readermock)])
-        final.save_new.assert_has_calls([mock.call(ensure_unique_name=True, name='Test output', owner_uuid='zzzzz-j7d0g-zzzzzzzzzzzzzzz')])
+        final.save_new.assert_has_calls([mock.call(ensure_unique_name=True, name='Test output', owner_uuid='zzzzz-j7d0g-zzzzzzzzzzzzzzz', storage_classes=['default'])])
         self.assertEqual("""{
     "bar": {
         "basename": "baz.txt",

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