[ARVADOS] updated: 1.3.0-2775-g0c2c8a174

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Summary of changes:

  discards  f1891356d894c0bebaf38ee4fdf03bed5550c577 (commit)
  discards  35ad6190cd68cbc544325b4fe6422b8142152aae (commit)
  discards  a220e4f0cc249bbab55399ecebd65e1294fa8c7c (commit)
       via  0c2c8a174afde6a1a2472ee346eb5a3fe0bc6114 (commit)
       via  b7c46875f592b2f959f504e7f583979a594d528f (commit)
       via  2b128f010976d8d4a55432e7b74349fd12362a93 (commit)
       via  150a601dbcaf6b999e54bd17d5152f15b626c7f3 (commit)

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 * -- * -- B -- O -- O -- O (f1891356d894c0bebaf38ee4fdf03bed5550c577)
            \
             N -- N -- N (0c2c8a174afde6a1a2472ee346eb5a3fe0bc6114)

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commit 0c2c8a174afde6a1a2472ee346eb5a3fe0bc6114
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Tue Jul 14 13:19:14 2020 -0400

    16584: Fix http tests for change in naming
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

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([

commit b7c46875f592b2f959f504e7f583979a594d528f
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Mon Jul 13 17:39:50 2020 -0400

    16584: Add --skip-schemas (passthrough to cwltool)
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index adbce90d8..8880f94c4 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -202,6 +202,14 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     parser.add_argument("--http-timeout", type=int,
                         default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
 
+    parser.add_argument(
+        "--skip-schemas",
+        action="store_true",
+        help="Skip loading of schemas",
+        default=False,
+        dest="skip_schemas",
+    )
+
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--trash-intermediate", action="store_true",
                         default=False, dest="trash_intermediate",

commit 2b128f010976d8d4a55432e7b74349fd12362a93
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Mon Jul 13 17:36:45 2020 -0400

    16584: collection name quote slashes in http_to_keep
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/http.py b/sdk/cwl/arvados_cwl/http.py
index 47a304372..dcc2a5119 100644
--- a/sdk/cwl/arvados_cwl/http.py
+++ b/sdk/cwl/arvados_cwl/http.py
@@ -16,6 +16,7 @@ import arvados.collection
 import urllib.parse
 import logging
 import calendar
+import urllib.parse
 
 logger = logging.getLogger('arvados.cwl-runner')
 
@@ -148,7 +149,9 @@ def http_to_keep(api, project_uuid, url, utcnow=datetime.datetime.utcnow):
                     logger.info("%d downloaded, %3.2f MiB/s", count, (bps / (1024*1024)))
                 checkpoint = loopnow
 
-    c.save_new(name="Downloaded from %s" % url, owner_uuid=project_uuid, ensure_unique_name=True)
+
+    collectionname = "Downloaded from %s" % urllib.parse.quote(url, safe='')
+    c.save_new(name=collectionname, owner_uuid=project_uuid, ensure_unique_name=True)
 
     api.collections().update(uuid=c.manifest_locator(), body={"collection":{"properties": properties}}).execute()
 

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