10291: Fix catching all exceptions in test case.

[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 e36a6076ab72de97ca446a34af2891906417250c..db1c494c44cb91cf8ccebeb693123583d75594c1 100644 (file)
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -22,7 +22,8 @@ class TestJob(unittest.TestCase):
         runner = mock.MagicMock()
         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
-        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
+        runner.num_retries = 0
+        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 
         tool = {
             "inputs": [],
@@ -70,7 +71,11 @@ class TestJob(unittest.TestCase):
         runner = mock.MagicMock()
         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
-        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("draft-3")
+        runner.num_retries = 0
+        arvados_cwl.add_arv_hints()
+
+        document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
+
 
         tool = {
             "inputs": [],
@@ -82,7 +87,8 @@ class TestJob(unittest.TestCase):
                 "tmpdirMin": 4000
             }, {
                 "class": "http://arvados.org/cwl#RuntimeConstraints",
-                "keep_cache": 512
+                "keep_cache": 512,
+                "outputDirType": "keep_output_dir"
             }, {
                 "class": "http://arvados.org/cwl#APIRequirement",
             }],
@@ -101,6 +107,7 @@ class TestJob(unittest.TestCase):
                 'script_parameters': {
                     'tasks': [{
                         'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
+                        'task.keepTmpOutput': True,
                         'command': ['ls']
                     }]
             },
@@ -122,8 +129,8 @@ class TestJob(unittest.TestCase):
                      ['script_version', 'in git', '9e5b98e8f5f4727856b53447191f9c06e3da2ba6'],
                      ['docker_image_locator', 'in docker', 'arvados/jobs']])
 
-    @mock.patch("arvados.collection.Collection")
-    def test_done(self, col):
+    @mock.patch("arvados.collection.CollectionReader")
+    def test_done(self, reader):
         api = mock.MagicMock()
 
         runner = mock.MagicMock()
@@ -132,7 +139,7 @@ class TestJob(unittest.TestCase):
         runner.num_retries = 0
         runner.ignore_docker_for_reuse = False
 
-        col().open.return_value = []
+        reader().open.return_value = []
         api.collections().list().execute.side_effect = ({"items": []},
                                                         {"items": [{"manifest_text": "XYZ"}]})
 
@@ -166,8 +173,8 @@ class TestJob(unittest.TestCase):
                   'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
                   'name': 'Output 9999999 of testjob'})
 
-    @mock.patch("arvados.collection.Collection")
-    def test_done_use_existing_collection(self, col):
+    @mock.patch("arvados.collection.CollectionReader")
+    def test_done_use_existing_collection(self, reader):
         api = mock.MagicMock()
 
         runner = mock.MagicMock()
@@ -175,7 +182,7 @@ class TestJob(unittest.TestCase):
         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.num_retries = 0
 
-        col().open.return_value = []
+        reader().open.return_value = []
         api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
 
         arvjob = arvados_cwl.ArvadosJob(runner)
@@ -209,8 +216,10 @@ class TestWorkflow(unittest.TestCase):
         arvados_cwl.add_arv_hints()
 
         runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
+
         runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
+        runner.num_retries = 0
         document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
 
         tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
@@ -247,7 +256,7 @@ class TestWorkflow(unittest.TestCase):
                                    'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
                                    'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
                                },
-                    'command': [u'cwltool', u'--no-container', u'--move-outputs', u'workflow.cwl#main', u'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'}]},
                 'runtime_constraints': {
                     'min_scratch_mb_per_node': 2048,