[ARVADOS] updated: 1.3.0-313-g7a9e57f98
Git user
git at public.curoverse.com
Mon Feb 11 11:32:17 EST 2019
Summary of changes:
sdk/cwl/arvados_cwl/arvcontainer.py | 3 +++
sdk/cwl/arvados_cwl/http.py | 2 +-
sdk/cwl/setup.py | 2 +-
sdk/cwl/tests/test_http.py | 6 +++---
sdk/cwl/tests/test_submit.py | 16 ++++++++--------
5 files changed, 16 insertions(+), 13 deletions(-)
via 7a9e57f98e2d5bad3dec7d17cfb9c86e5c5c927c (commit)
via a394a4df81fd51691df7742f0c71ba91afbacefc (commit)
via 171b9ac5962c21dead1d04f4c53460a81b9b9993 (commit)
from cdd31206b8c228ffcdc6f0ab7f0017d537836678 (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 7a9e57f98e2d5bad3dec7d17cfb9c86e5c5c927c
Merge: cdd31206b a394a4df8
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Mon Feb 11 11:32:01 2019 -0500
Merge branch '14725-wes' refs #14725
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
commit a394a4df81fd51691df7742f0c71ba91afbacefc
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Mon Feb 11 11:23:48 2019 -0500
14725: Fix tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/test_http.py b/sdk/cwl/tests/test_http.py
index 88bd49fcd..4119fee38 100644
--- a/sdk/cwl/tests/test_http.py
+++ b/sdk/cwl/tests/test_http.py
@@ -60,7 +60,7 @@ class TestHttpToKeep(unittest.TestCase):
getmock.assert_called_with("http://example.com/file1.txt", stream=True, allow_redirects=True)
- cm.open.assert_called_with("file1.txt", "w")
+ cm.open.assert_called_with("file1.txt", "wb")
cm.save_new.assert_called_with(name="Downloaded from http://example.com/file1.txt",
owner_uuid=None, ensure_unique_name=True)
@@ -188,7 +188,7 @@ class TestHttpToKeep(unittest.TestCase):
getmock.assert_called_with("http://example.com/file1.txt", stream=True, allow_redirects=True)
- cm.open.assert_called_with("file1.txt", "w")
+ cm.open.assert_called_with("file1.txt", "wb")
cm.save_new.assert_called_with(name="Downloaded from http://example.com/file1.txt",
owner_uuid=None, ensure_unique_name=True)
@@ -279,7 +279,7 @@ class TestHttpToKeep(unittest.TestCase):
getmock.assert_called_with("http://example.com/download?fn=/file1.txt", stream=True, allow_redirects=True)
- cm.open.assert_called_with("file1.txt", "w")
+ cm.open.assert_called_with("file1.txt", "wb")
cm.save_new.assert_called_with(name="Downloaded from http://example.com/download?fn=/file1.txt",
owner_uuid=None, ensure_unique_name=True)
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 782282d2a..39117d86e 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -512,7 +512,7 @@ class TestSubmit(unittest.TestCase):
body=JsonDiffMatcher(expect_pipeline))
@stubs
- def test_submit_container(self, stubs):
+ def test_submit_container(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
@@ -559,7 +559,7 @@ class TestSubmit(unittest.TestCase):
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_container_request_uuid + '\n')
+ stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
@stubs
@@ -602,7 +602,7 @@ class TestSubmit(unittest.TestCase):
["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
-
+
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
@@ -620,7 +620,7 @@ class TestSubmit(unittest.TestCase):
@stubs
def test_submit_container_output_name(self, stubs):
output_name = "test_output_name"
-
+
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
@@ -642,7 +642,7 @@ class TestSubmit(unittest.TestCase):
self.assertEqual(exited, 0)
@stubs
- def test_submit_storage_classes(self, stubs):
+ def test_submit_storage_classes(self, stubs):
exited = arvados_cwl.main(
["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
@@ -726,7 +726,7 @@ class TestSubmit(unittest.TestCase):
["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
-
+
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
@@ -1394,7 +1394,7 @@ class TestSubmit(unittest.TestCase):
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
stubs.api.container_requests().update.assert_called_with(
- uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec), cluster_id="zzzzz")
+ uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
@@ -1541,7 +1541,7 @@ class TestCreateTemplate(unittest.TestCase):
self.assertEqual(stubs.capture_stdout.getvalue(),
self.existing_template_uuid + '\n')
self.assertEqual(exited, 0)
-
+
class TestCreateWorkflow(unittest.TestCase):
existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
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