Merge remote-tracking branch 'origin/master' into 14645-fuse-operations-reporting

[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 1c45b384f5b50facee20280c8463ea22e5e8b2f1..022d75be11a09031746adf7a39975793ec293e83 100644 (file)
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -2,6 +2,11 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
+from future import standard_library
+standard_library.install_aliases()
+from builtins import str
+from builtins import next
+
 import functools
 import json
 import logging
@@ -9,16 +14,18 @@ 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)
@@ -41,7 +48,7 @@ class TestJob(unittest.TestCase):
         runtimeContext = arvados_cwl.context.ArvRuntimeContext(
             {"work_api": "jobs",
              "basedir": "",
-             "name": "test_run_"+str(enable_reuse),
+             "name": "test_run_job_"+str(enable_reuse),
              "make_fs_access": make_fs_access,
              "enable_reuse": enable_reuse,
              "priority": 500})
@@ -124,7 +131,7 @@ class TestJob(unittest.TestCase):
                     # sharing link on the job
                     runner.api.links().create.side_effect = ApiError(
                         mock.MagicMock(return_value={'status': 403}),
-                        'Permission denied')
+                        bytes(b'Permission denied'))
                     j.run(runtimeContext)
                 else:
                     assert not runner.api.links().create.called
@@ -211,11 +218,12 @@ class TestJob(unittest.TestCase):
         runner.num_retries = 0
         runner.ignore_docker_for_reuse = False
 
-        reader().open.return_value = StringIO.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
+        reader().keys.return_value = "log.txt"
+        reader().open.return_value = io.StringIO(
+            str(u"""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
-        """)
+        """))
         api.collections().list().execute.side_effect = ({"items": []},
                                                         {"items": [{"manifest_text": "XYZ"}]},
                                                         {"items": []},
@@ -284,11 +292,12 @@ class TestJob(unittest.TestCase):
         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.num_retries = 0
 
-        reader().open.return_value = StringIO.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
+        reader().keys.return_value = "log.txt"
+        reader().open.return_value = io.StringIO(
+            str(u"""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
-        """)
+        """))
 
         api.collections().list().execute.side_effect = (
             {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},
@@ -354,7 +363,7 @@ class TestWorkflow(unittest.TestCase):
         runtimeContext = arvados_cwl.context.ArvRuntimeContext(
             {"work_api": "jobs",
              "basedir": "",
-             "name": "test_run_"+str(enable_reuse),
+             "name": "test_run_wf_"+str(enable_reuse),
              "make_fs_access": make_fs_access,
              "enable_reuse": enable_reuse,
              "priority": 500})
@@ -372,7 +381,7 @@ 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"]]
@@ -388,14 +397,16 @@ 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)
         arvtool.formatgraph = None
         it = arvtool.job({}, mock.MagicMock(), runtimeContext)
 
-        it.next().run(runtimeContext)
-        it.next().run(runtimeContext)
+        next(it).run(runtimeContext)
+        next(it).run(runtimeContext)
 
         with open("tests/wf/scatter2_subwf.cwl") as f:
             subwf = StripYAMLComments(f.read())
@@ -411,8 +422,8 @@ 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'}]},
@@ -429,16 +440,17 @@ 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(
+bytes(b'''{
   "fileblub": {
     "basename": "token.txt",
     "class": "File",
-    "location": "/keep/99999999999999999999999999999999+118/token.txt"
+    "location": "/keep/99999999999999999999999999999999+118/token.txt",
+    "size": 0
   },
   "sleeptime": 5
-}''')])
+}'''))])
 
     # The test passes no builder.resources
     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@@ -451,7 +463,7 @@ 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"]]
@@ -467,13 +479,14 @@ 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
         it = arvtool.job({}, mock.MagicMock(), runtimeContext)
-        it.next().run(runtimeContext)
-        it.next().run(runtimeContext)
+        
+        next(it).run(runtimeContext)
+        next(it).run(runtimeContext)
 
         with open("tests/wf/echo-subwf.cwl") as f:
             subwf = StripYAMLComments(f.read())
@@ -489,8 +502,8 @@ 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'}]},
@@ -513,5 +526,5 @@ 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')