13306: Changes to arvados-cwl-runner code after running futurize --stage2

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

diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index 4473b88ca0d785dbb2eaff961bf64fd21c25c280..387d12f388dc4fce6af87eb4de7a2e7dd267ce07 100644 (file)
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -1,3 +1,6 @@
+from future import standard_library
+standard_library.install_aliases()
+from builtins import str
 # Copyright (C) The Arvados Authors. All rights reserved.
 #
 # SPDX-License-Identifier: Apache-2.0
@@ -9,16 +12,18 @@ import mock
 import os
 import unittest
 import copy
-import StringIO
+import io
 
 import arvados
 import arvados_cwl
+import arvados_cwl.executor
 import cwltool.process
 from arvados.errors import ApiError
 from schema_salad.ref_resolver import Loader
 from schema_salad.sourceline import cmap
 from .mock_discovery import get_rootDesc
 from .matcher import JsonDiffMatcher, StripYAMLComments
+from .test_container import CollectionMock
 
 if not os.getenv('ARVADOS_DEBUG'):
     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
@@ -211,7 +216,7 @@ class TestJob(unittest.TestCase):
         runner.num_retries = 0
         runner.ignore_docker_for_reuse = False
 
-        reader().open.return_value = StringIO.StringIO(
+        reader().open.return_value = io.StringIO(
             """2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.tmpdir)=/tmp/crunch-job-task-work/compute3.1/tmpdir
 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.outdir)=/tmp/crunch-job-task-work/compute3.1/outdir
 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
@@ -284,7 +289,7 @@ class TestJob(unittest.TestCase):
         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.num_retries = 0
 
-        reader().open.return_value = StringIO.StringIO(
+        reader().open.return_value = io.StringIO(
             """2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.tmpdir)=/tmp/crunch-job-task-work/compute3.1/tmpdir
 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.outdir)=/tmp/crunch-job-task-work/compute3.1/outdir
 2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
@@ -372,7 +377,7 @@ class TestWorkflow(unittest.TestCase):
         api = mock.MagicMock()
         api._rootDesc = get_rootDesc()
 
-        runner = arvados_cwl.ArvCwlRunner(api)
+        runner = arvados_cwl.executor.ArvCwlExecutor(api)
         self.assertEqual(runner.work_api, 'jobs')
 
         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
@@ -388,7 +393,8 @@ class TestWorkflow(unittest.TestCase):
         tool, metadata = loadingContext.loader.resolve_ref("tests/wf/scatter2.cwl")
         metadata["cwlVersion"] = tool["cwlVersion"]
 
-        mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+        mockc = mock.MagicMock()
+        mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mockc, *args, **kwargs)
         mockcollectionreader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "token.txt")
 
         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
@@ -412,8 +418,8 @@ class TestWorkflow(unittest.TestCase):
                         'HOME': '$(task.outdir)',
                         'TMPDIR': '$(task.tmpdir)'},
                                'task.vwd': {
-                                   'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
-                                   'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+                                   'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl',
+                                   'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml'
                                },
                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
                     'task.stdout': 'cwl.output.json'}]},
@@ -430,8 +436,8 @@ class TestWorkflow(unittest.TestCase):
                      ['docker_image_locator', 'in docker', 'arvados/jobs']],
             find_or_create=True)
 
-        mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
-        mockcollection().open().__enter__().write.assert_has_calls([mock.call(
+        mockc.open().__enter__().write.assert_has_calls([mock.call(subwf)])
+        mockc.open().__enter__().write.assert_has_calls([mock.call(
 '''{
   "fileblub": {
     "basename": "token.txt",
@@ -453,7 +459,7 @@ class TestWorkflow(unittest.TestCase):
         api = mock.MagicMock()
         api._rootDesc = get_rootDesc()
 
-        runner = arvados_cwl.ArvCwlRunner(api)
+        runner = arvados_cwl.executor.ArvCwlExecutor(api)
         self.assertEqual(runner.work_api, 'jobs')
 
         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
@@ -469,7 +475,7 @@ class TestWorkflow(unittest.TestCase):
         tool, metadata = loadingContext.loader.resolve_ref("tests/wf/echo-wf.cwl")
         metadata["cwlVersion"] = tool["cwlVersion"]
 
-        mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+        mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mock.MagicMock(), *args, **kwargs)
 
         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
         arvtool.formatgraph = None
@@ -491,8 +497,8 @@ class TestWorkflow(unittest.TestCase):
                         'HOME': '$(task.outdir)',
                         'TMPDIR': '$(task.tmpdir)'},
                                'task.vwd': {
-                                   'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
-                                   'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+                                   'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl',
+                                   'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml'
                                },
                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
                     'task.stdout': 'cwl.output.json'}]},
@@ -515,5 +521,5 @@ class TestWorkflow(unittest.TestCase):
         api = mock.MagicMock()
         api._rootDesc = copy.deepcopy(get_rootDesc())
         del api._rootDesc.get('resources')['jobs']['methods']['create']
-        runner = arvados_cwl.ArvCwlRunner(api)
+        runner = arvados_cwl.executor.ArvCwlExecutor(api)
         self.assertEqual(runner.work_api, 'containers')