[ARVADOS] updated: 1.3.0-2774-gf1891356d
Git user
git at public.arvados.org
Tue Jul 14 17:20:22 UTC 2020
Summary of changes:
sdk/cwl/arvados_cwl/executor.py | 2 +-
sdk/cwl/tests/test_http.py | 6 +++---
sdk/cwl/tests/test_submit.py | 23 ++++++++++++++++-------
3 files changed, 20 insertions(+), 11 deletions(-)
via f1891356d894c0bebaf38ee4fdf03bed5550c577 (commit)
from 35ad6190cd68cbc544325b4fe6422b8142152aae (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 f1891356d894c0bebaf38ee4fdf03bed5550c577
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Tue Jul 14 13:19:14 2020 -0400
16584: Don't consume exception in set_crunch_output
Fix a couple of incorrect tests that were hidden by this.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index ec91eea6a..e8d1347dd 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -507,7 +507,7 @@ The 'jobs' API is no longer supported.
}).execute(num_retries=self.num_retries)
except Exception:
logger.exception("Setting container output")
- return
+ raise
def apply_reqs(self, job_order_object, tool):
if "https://w3id.org/cwl/cwl#requirements" in job_order_object:
diff --git a/sdk/cwl/tests/test_http.py b/sdk/cwl/tests/test_http.py
index 4119fee38..650b5f059 100644
--- a/sdk/cwl/tests/test_http.py
+++ b/sdk/cwl/tests/test_http.py
@@ -61,7 +61,7 @@ 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", "wb")
- cm.save_new.assert_called_with(name="Downloaded from http://example.com/file1.txt",
+ cm.save_new.assert_called_with(name="Downloaded from http%3A%2F%2Fexample.com%2Ffile1.txt",
owner_uuid=None, ensure_unique_name=True)
api.collections().update.assert_has_calls([
@@ -189,7 +189,7 @@ 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", "wb")
- cm.save_new.assert_called_with(name="Downloaded from http://example.com/file1.txt",
+ cm.save_new.assert_called_with(name="Downloaded from http%3A%2F%2Fexample.com%2Ffile1.txt",
owner_uuid=None, ensure_unique_name=True)
api.collections().update.assert_has_calls([
@@ -280,7 +280,7 @@ 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", "wb")
- cm.save_new.assert_called_with(name="Downloaded from http://example.com/download?fn=/file1.txt",
+ cm.save_new.assert_called_with(name="Downloaded from http%3A%2F%2Fexample.com%2Fdownload%3Ffn%3D%2Ffile1.txt",
owner_uuid=None, ensure_unique_name=True)
api.collections().update.assert_has_calls([
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 562664c69..0698db70f 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -527,9 +527,12 @@ class TestSubmit(unittest.TestCase):
@mock.patch("arvados_cwl.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
- @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
+ @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
@stubs
def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+ final_output_c = arvados.collection.Collection()
+ make_output.return_value = ({},final_output_c)
+
def set_final_output(job_order, output_callback, runtimeContext):
output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
return []
@@ -538,16 +541,19 @@ class TestSubmit(unittest.TestCase):
exited = arvados_cwl.main(
["--debug", "--local", "--storage-classes=foo",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
self.assertEqual(exited, 0)
@mock.patch("arvados_cwl.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
- @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
+ @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
@stubs
def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+ final_output_c = arvados.collection.Collection()
+ make_output.return_value = ({},final_output_c)
+
def set_final_output(job_order, output_callback, runtimeContext):
output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
return []
@@ -556,7 +562,7 @@ class TestSubmit(unittest.TestCase):
exited = arvados_cwl.main(
["--debug", "--local",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
self.assertEqual(exited, 0)
@@ -1103,7 +1109,10 @@ class TestSubmit(unittest.TestCase):
"outputs": [
{
"id": "#secret_job.cwl/out",
- "type": "stdout"
+ "type": "File",
+ "outputBinding": {
+ "glob": "hashed_example.txt"
+ }
}
],
"stdout": "hashed_example.txt",
@@ -1312,7 +1321,7 @@ class TestSubmit(unittest.TestCase):
stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 1)
- self.assertRegexpMatches(
+ self.assertRegex(
re.sub(r'[ \n]+', ' ', capture_stderr.getvalue()),
r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99")
finally:
@@ -1335,7 +1344,7 @@ class TestSubmit(unittest.TestCase):
try:
self.assertEqual(exited, 1)
- self.assertRegexpMatches(
+ self.assertRegex(
capture_stderr.getvalue(),
r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found")
finally:
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