[ARVADOS] updated: 1.3.0-531-ga9a3acde6

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/runner.py |  3 +++
 sdk/cwl/tests/test_submit.py  | 17 +++++++++++++----
 2 files changed, 16 insertions(+), 4 deletions(-)

       via  a9a3acde6863a8b0885bbdc0d6d81fcfa473eb59 (commit)
      from  b65b36691117322a34170f28ae1997073f2829f0 (commit)

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commit a9a3acde6863a8b0885bbdc0d6d81fcfa473eb59
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Fri Mar 15 10:54:59 2019 -0400

    14322: Fix noisy unicode logging error in tests, add comments
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index d30445ab3..9385bde63 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -174,6 +174,9 @@ def upload_dependencies(arvrunner, name, document_loader,
     uuid_map = {}
     fetch_uuids = list(uuids.keys())
     while fetch_uuids:
+        # For a large number of fetch_uuids, API server may limit
+        # response size, so keep fetching from API server has nothing
+        # more to give us.
         lookups = arvrunner.api.collections().list(
             filters=[["uuid", "in", fetch_uuids]],
             count="none",
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 4e4ab7277..9535f6ba2 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -18,7 +18,16 @@ import mock
 import sys
 import unittest
 
-from io import BytesIO, StringIO
+from io import BytesIO
+
+# StringIO.StringIO and io.StringIO have different behavior write() is
+# called with both python2 (byte) strings and unicode strings
+# (specifically there's some logging in cwltool that causes trouble).
+# This isn't a problem on python3 because all string are unicode.
+if sys.version_info[0] < 3:
+    from StringIO import StringIO
+else:
+    from io import StringIO
 
 import arvados
 import arvados.collection
@@ -1479,7 +1488,7 @@ class TestSubmit(unittest.TestCase):
         stubs.api.collections().list.side_effect = list_side_effect
 
         for infile in ("tests/submit_test_job_with_mismatched_uuids.json", "tests/submit_test_job_with_inconsistent_uuids.json"):
-            capture_stderr = io.StringIO()
+            capture_stderr = StringIO()
             cwltool_logger = logging.getLogger('cwltool')
             stderr_logger = logging.StreamHandler(capture_stderr)
             cwltool_logger.addHandler(stderr_logger)
@@ -1501,8 +1510,8 @@ class TestSubmit(unittest.TestCase):
     @stubs
     def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
         collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
+        capture_stderr = StringIO()
 
-        capture_stderr = io.StringIO()
         cwltool_logger = logging.getLogger('cwltool')
         stderr_logger = logging.StreamHandler(capture_stderr)
         cwltool_logger.addHandler(stderr_logger)
@@ -1704,7 +1713,7 @@ class TestCreateWorkflow(unittest.TestCase):
 
     @stubs
     def test_incompatible_api(self, stubs):
-        capture_stderr = io.StringIO()
+        capture_stderr = StringIO()
         acr_logger = logging.getLogger('arvados.cwl-runner')
         stderr_logger = logging.StreamHandler(capture_stderr)
         acr_logger.addHandler(stderr_logger)

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