Arvados-DCO-1.1-Signed-off-by: Radhika Chippada <radhika@curoverse.com>

[arvados.git] / sdk / cwl / tests / test_pathmapper.py

diff --git a/sdk/cwl/tests/test_pathmapper.py b/sdk/cwl/tests/test_pathmapper.py
index 57958f78d0a41a97b9d5b0aa5f10a2cf10563b22..9649b838726d845ebe56418934852fe080f2dfc7 100644 (file)
--- a/sdk/cwl/tests/test_pathmapper.py
+++ b/sdk/cwl/tests/test_pathmapper.py
@@ -1,3 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 import functools
 import mock
 import sys
@@ -12,18 +16,20 @@ import arvados.collection
 import arvados_cwl
 
 from cwltool.pathmapper import MapperEnt
+from .mock_discovery import get_rootDesc
 
 from arvados_cwl.pathmapper import ArvPathMapper
 
-def upload_mock(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None):
+def upload_mock(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None, collection=None):
     pdh = "99999999999999999999999999999991+99"
     for c in files:
+        c.keepref = "%s/%s" % (pdh, os.path.basename(c.fn))
         c.fn = fnPattern % (pdh, os.path.basename(c.fn))
 
 class TestPathmap(unittest.TestCase):
     def setUp(self):
         self.api = mock.MagicMock()
-        self.api._rootDesc = arvados.api('v1')._rootDesc
+        self.api._rootDesc = get_rootDesc()
 
     def test_keepref(self):
         """Test direct keep references."""
@@ -35,23 +41,29 @@ class TestPathmap(unittest.TestCase):
             "location": "keep:99999999999999999999999999999991+99/hw.py"
         }], "", "/test/%s", "/test/%s/%s")
 
-        self.assertEqual({'keep:99999999999999999999999999999991+99/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
+        self.assertEqual({'keep:99999999999999999999999999999991+99/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
                          p._pathmap)
 
     @mock.patch("arvados.commands.run.uploadfiles")
-    def test_upload(self, upl):
+    @mock.patch("arvados.commands.run.statfile")
+    def test_upload(self, statfile, upl):
         """Test pathmapper uploading files."""
 
         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
 
+        def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)", raiseOSError=False):
+            st = arvados.commands.run.UploadFile("", "tests/hw.py")
+            return st
+
         upl.side_effect = upload_mock
+        statfile.side_effect = statfile_mock
 
         p = ArvPathMapper(arvrunner, [{
             "class": "File",
-            "location": "tests/hw.py"
+            "location": "file:tests/hw.py"
         }], "", "/test/%s", "/test/%s/%s")
 
-        self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
+        self.assertEqual({'file:tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
                          p._pathmap)
 
     @mock.patch("arvados.commands.run.uploadfiles")
@@ -59,16 +71,16 @@ class TestPathmap(unittest.TestCase):
         """Test pathmapper handling previously uploaded files."""
 
         arvrunner = arvados_cwl.ArvCwlRunner(self.api)
-        arvrunner.add_uploaded('tests/hw.py', MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='', type='File'))
+        arvrunner.add_uploaded('file:tests/hw.py', MapperEnt(resolved='keep:99999999999999999999999999999992+99/hw.py', target='', type='File', staged=True))
 
         upl.side_effect = upload_mock
 
         p = ArvPathMapper(arvrunner, [{
             "class": "File",
-            "location": "tests/hw.py"
+            "location": "file:tests/hw.py"
         }], "", "/test/%s", "/test/%s/%s")
 
-        self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
+        self.assertEqual({'file:tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999992+99/hw.py', target='/test/99999999999999999999999999999992+99/hw.py', type='File', staged=True)},
                          p._pathmap)
 
     @mock.patch("arvados.commands.run.uploadfiles")
@@ -79,7 +91,7 @@ class TestPathmap(unittest.TestCase):
 
         # An ArvFile object returned from arvados.commands.run.statfile means the file is located on a
         # keep mount, so we can construct a direct reference directly without upload.
-        def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
+        def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)", raiseOSError=False):
             st = arvados.commands.run.ArvFile("", fnPattern % ("99999999999999999999999999999991+99", "hw.py"))
             return st
 
@@ -88,8 +100,21 @@ class TestPathmap(unittest.TestCase):
 
         p = ArvPathMapper(arvrunner, [{
             "class": "File",
-            "location": "tests/hw.py"
+            "location": "file:tests/hw.py"
         }], "", "/test/%s", "/test/%s/%s")
 
-        self.assertEqual({'tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File')},
+        self.assertEqual({'file:tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
                          p._pathmap)
+
+    @mock.patch("os.stat")
+    def test_missing_file(self, stat):
+        """Test pathmapper handling missing references."""
+        arvrunner = arvados_cwl.ArvCwlRunner(self.api)
+
+        stat.side_effect = OSError(2, "No such file or directory")
+
+        with self.assertRaises(OSError):
+            p = ArvPathMapper(arvrunner, [{
+                "class": "File",
+                "location": "file:tests/hw.py"
+            }], "", "/test/%s", "/test/%s/%s")