[ARVADOS] updated: 90c48f84391d6b4d6b8ed366d5a42d24bf6c696f

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py   |  4 +++-
 sdk/cwl/tests/test_make_output.py |  7 +++---
 sdk/cwl/tests/test_submit.py      | 46 +++++++++++++++++++++++++++++++++++++++
 3 files changed, 53 insertions(+), 4 deletions(-)

       via  90c48f84391d6b4d6b8ed366d5a42d24bf6c696f (commit)
      from  1e6d7656fbfd1f954571157fc7e7e4f75ea5911e (commit)

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commit 90c48f84391d6b4d6b8ed366d5a42d24bf6c696f
Author: Jiayong Li <jiayong at math.mit.edu>
Date:   Mon Nov 14 15:30:46 2016 -0500

    Add num_tries to adding tags and tests for container API

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 501bad5..6778eb0 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -238,7 +238,9 @@ class ArvCwlRunner(object):
         final_uuid = final.manifest_locator()
         tags = tagsString.split(',')
         for tag in tags:
-             self.api.links().create(body={"head_uuid": final_uuid, "link_class": "tag", "name": tag}).execute()
+             self.api.links().create(body={
+                "head_uuid": final_uuid, "link_class": "tag", "name": tag
+                }).execute(num_retries=self.num_retries)
 
         self.final_output_collection = final
 
diff --git a/sdk/cwl/tests/test_make_output.py b/sdk/cwl/tests/test_make_output.py
index 153de7b..a1cb605 100644
--- a/sdk/cwl/tests/test_make_output.py
+++ b/sdk/cwl/tests/test_make_output.py
@@ -28,6 +28,7 @@ class TestMakeOutput(unittest.TestCase):
         reader.return_value = readermock
 
         final_uuid = final.manifest_locator()
+        num_retries = runner.num_retries
 
         cwlout = StringIO.StringIO()
         openmock = mock.MagicMock()
@@ -64,6 +65,6 @@ class TestMakeOutput(unittest.TestCase):
 
         self.assertIs(final, runner.final_output_collection)
         self.assertIs(final_uuid, runner.final_output_collection.manifest_locator())
-        self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag0"}), mock.call().execute()])
-        self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag1"}), mock.call().execute()])
-        self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag2"}), mock.call().execute()])
+        self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag0"}), mock.call().execute(num_retries=num_retries)])
+        self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag1"}), mock.call().execute(num_retries=num_retries)])
+        self.api.links().create.assert_has_calls([mock.call(body={"head_uuid": final_uuid, "link_class": "tag", "name": "tag2"}), mock.call().execute(num_retries=num_retries)])
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index ebb8360..085509f 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -394,6 +394,52 @@ class TestSubmit(unittest.TestCase):
         self.assertEqual(capture_stdout.getvalue(),
                          stubs.expect_container_request_uuid + '\n')
 
+    @stubs
+    def test_submit_container_output_name(self, stubs):
+        output_name = "test_output_name"
+
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["owner_uuid"] = stubs.fake_user_uuid
+        stubs.api.container_requests().create.assert_called_with(
+            body=expect_container)
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+    @stubs
+    def test_submit_container_output_tags(self, stubs):
+        output_tags = "tag0,tag1,tag2"
+
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        stubs.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-tags="+output_tags, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json']
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["owner_uuid"] = stubs.fake_user_uuid
+        stubs.api.container_requests().create.assert_called_with(
+            body=expect_container)
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
     @mock.patch("arvados.commands.keepdocker.find_one_image_hash")
     @mock.patch("cwltool.docker.get_image")
     @mock.patch("arvados.api")

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