[ARVADOS] updated: 1.1.0-14-g0bb435a

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/fsaccess.py               | 12 ++++++------
 sdk/cwl/tests/12418-glob-empty-collection.cwl | 20 ++++++++++++++++++++
 sdk/cwl/tests/arvados-tests.yml               |  6 ++++++
 sdk/python/tests/test_collections.py          |  4 ++++
 4 files changed, 36 insertions(+), 6 deletions(-)
 create mode 100644 sdk/cwl/tests/12418-glob-empty-collection.cwl

       via  0bb435a47e427b12fa2351141a22a1ba1e28a49d (commit)
       via  29defca7cc4c36c110a5a5da60bbf4fca7528af1 (commit)
       via  c621fc52c25af82c90d435598134d1db7ba8e346 (commit)
      from  455006efb88b2dbf7b489831d06afb850ac4e9aa (commit)

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not appeared on any other notification email; so we list those
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commit 0bb435a47e427b12fa2351141a22a1ba1e28a49d
Merge: 455006e 29defca
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Oct 10 14:04:33 2017 -0400

    Merge branch '12418-glob-empty-collection' closes #12418
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>


commit 29defca7cc4c36c110a5a5da60bbf4fca7528af1
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Oct 10 14:03:55 2017 -0400

    12418: Add regression test for glob output on empty collection.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/tests/12418-glob-empty-collection.cwl b/sdk/cwl/tests/12418-glob-empty-collection.cwl
new file mode 100644
index 0000000..6c9e7f7
--- /dev/null
+++ b/sdk/cwl/tests/12418-glob-empty-collection.cwl
@@ -0,0 +1,20 @@
+{
+   "cwlVersion": "v1.0",
+      "arguments": [
+        "true"
+      ],
+      "class": "CommandLineTool",
+      "inputs": [],
+      "outputs": [
+        {
+          "id": "out",
+          "outputBinding": {
+            "glob": "*.txt"
+          },
+          "type": [
+            "null",
+            "File"
+          ]
+        }
+      ]
+}
\ No newline at end of file
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 2f1429e..a0de236 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -111,3 +111,9 @@
   }
   tool: 12213-keepref-wf.cwl
   doc: "Test manipulating keep references with expression tools"
+
+- job: null
+  output:
+    out: null
+  tool: 12418-glob-empty-collection.cwl
+  doc: "Test glob output on empty collection"

commit c621fc52c25af82c90d435598134d1db7ba8e346
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Oct 10 11:19:47 2017 -0400

    12418: Explicitly check if collection is not None
    
    The empty collection evaluates to False, so it is necessary to explicitly check
    for "not None".
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 08e203b..5bdd8dd 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -81,14 +81,14 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     def glob(self, pattern):
         collection, rest = self.get_collection(pattern)
-        if collection and not rest:
+        if collection is not None and not rest:
             return [pattern]
         patternsegments = rest.split("/")
         return self._match(collection, patternsegments, "keep:" + collection.manifest_locator())
 
     def open(self, fn, mode):
         collection, rest = self.get_collection(fn)
-        if collection:
+        if collection is not None:
             return collection.open(rest, mode)
         else:
             return super(CollectionFsAccess, self).open(self._abs(fn), mode)
@@ -105,7 +105,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     def isfile(self, fn):  # type: (unicode) -> bool
         collection, rest = self.get_collection(fn)
-        if collection:
+        if collection is not None:
             if rest:
                 return isinstance(collection.find(rest), arvados.arvfile.ArvadosFile)
             else:
@@ -115,7 +115,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     def isdir(self, fn):  # type: (unicode) -> bool
         collection, rest = self.get_collection(fn)
-        if collection:
+        if collection is not None:
             if rest:
                 return isinstance(collection.find(rest), arvados.collection.RichCollectionBase)
             else:
@@ -125,7 +125,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     def listdir(self, fn):  # type: (unicode) -> List[unicode]
         collection, rest = self.get_collection(fn)
-        if collection:
+        if collection is not None:
             if rest:
                 dir = collection.find(rest)
             else:
@@ -147,7 +147,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
         if path.startswith("$(task.tmpdir)") or path.startswith("$(task.outdir)"):
             return path
         collection, rest = self.get_collection(path)
-        if collection:
+        if collection is not None:
             return path
         else:
             return os.path.realpath(path)
diff --git a/sdk/python/tests/test_collections.py b/sdk/python/tests/test_collections.py
index e8c6dd1..5f40bb2 100644
--- a/sdk/python/tests/test_collections.py
+++ b/sdk/python/tests/test_collections.py
@@ -97,6 +97,8 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers,
         self.assertEqual(stream0.readfrom(2**26, 0),
                          b'',
                          'reading zero bytes should have returned empty string')
+        self.assertEqual(3, len(cr))
+        self.assertTrue(cr)
 
     def _test_subset(self, collection, expected):
         cr = arvados.CollectionReader(collection, self.api_client)
@@ -632,6 +634,8 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin):
         reader = arvados.CollectionReader('d41d8cd98f00b204e9800998ecf8427e+0',
                                           api_client=client)
         self.assertEqual('', reader.manifest_text())
+        self.assertEqual(0, len(reader))
+        self.assertFalse(reader)
 
     def test_api_response(self):
         client = self.api_client_mock()

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