Merge branch 'govendor'

[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 5cd7f2a7b6706ccc5435083f9cd91902e2795547..faac1f77a640456b5f8671e1735629b713d04b42 100644 (file)
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -1,3 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 import functools
 import json
 import logging
@@ -10,10 +14,11 @@ import StringIO
 import arvados
 import arvados_cwl
 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
+from .matcher import JsonDiffMatcher, StripYAMLComments
 
 if not os.getenv('ARVADOS_DEBUG'):
     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
@@ -86,11 +91,19 @@ class TestJob(unittest.TestCase):
                 if enable_reuse:
                     runner.api.links().create.assert_called_with(
                         body=JsonDiffMatcher({
-                            'link_class': 'can_read',
+                            'link_class': 'permission',
+                            'name': 'can_read',
                             "tail_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
                             "head_uuid": "zzzzz-819sb-yyyyyyyyyyyyyyy",
                         })
                     )
+                    # Simulate an API excepction when trying to create a
+                    # sharing link on the job
+                    runner.api.links().create.side_effect = ApiError(
+                        mock.MagicMock(return_value={'status': 403}),
+                        'Permission denied')
+                    j.run(enable_reuse=enable_reuse)
+                    j.output_callback.assert_called_with({}, 'success')
                 else:
                     assert not runner.api.links().create.called
 
@@ -124,6 +137,10 @@ class TestJob(unittest.TestCase):
                 "outputDirType": "keep_output_dir"
             }, {
                 "class": "http://arvados.org/cwl#APIRequirement",
+            },
+            {
+                "class": "http://arvados.org/cwl#ReuseRequirement",
+                "enableReuse": False
             }],
             "baseCommand": "ls"
         }
@@ -133,7 +150,7 @@ class TestJob(unittest.TestCase):
                                                  make_fs_access=make_fs_access, loader=Loader({}))
         arvtool.formatgraph = None
         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
-            j.run()
+            j.run(enable_reuse=True)
         runner.api.jobs().create.assert_called_with(
             body=JsonDiffMatcher({
                 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
@@ -157,7 +174,7 @@ class TestJob(unittest.TestCase):
                     'keep_cache_mb_per_task': 512
                 }
             }),
-            find_or_create=True,
+            find_or_create=False,
             filters=[['repository', '=', 'arvados'],
                      ['script', '=', 'crunchrunner'],
                      ['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
@@ -289,9 +306,10 @@ class TestJob(unittest.TestCase):
 class TestWorkflow(unittest.TestCase):
     # The test passes no builder.resources
     # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+    @mock.patch("arvados.collection.CollectionReader")
     @mock.patch("arvados.collection.Collection")
     @mock.patch('arvados.commands.keepdocker.list_images_in_arv')
-    def test_run(self, list_images_in_arv, mockcollection):
+    def test_run(self, list_images_in_arv, mockcollection, mockcollectionreader):
         arvados_cwl.add_arv_hints()
 
         api = mock.MagicMock()
@@ -302,19 +320,25 @@ class TestWorkflow(unittest.TestCase):
 
         list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
         runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
+        runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]}
 
         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")
 
+        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+                                         collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
+        document_loader.fetcher_constructor = functools.partial(arvados_cwl.CollectionFetcher, api_client=api, fs_access=make_fs_access(""))
+        document_loader.fetcher = document_loader.fetcher_constructor(document_loader.cache, document_loader.session)
+        document_loader.fetch_text = document_loader.fetcher.fetch_text
+        document_loader.check_exists = document_loader.fetcher.check_exists
+
         tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
         metadata["cwlVersion"] = tool["cwlVersion"]
 
         mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
 
-        make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
-                                         collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
                                               basedir="", make_fs_access=make_fs_access, loader=document_loader,
                                               makeTool=runner.arv_make_tool, metadata=metadata)
@@ -324,7 +348,7 @@ class TestWorkflow(unittest.TestCase):
         it.next().run()
 
         with open("tests/wf/scatter2_subwf.cwl") as f:
-            subwf = f.read()
+            subwf = StripYAMLComments(f.read())
 
         runner.api.jobs().create.assert_called_with(
             body=JsonDiffMatcher({
@@ -358,6 +382,11 @@ class TestWorkflow(unittest.TestCase):
         mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
         mockcollection().open().__enter__().write.assert_has_calls([mock.call(
 '''{
+  "fileblub": {
+    "basename": "token.txt",
+    "class": "File",
+    "location": "/keep/99999999999999999999999999999999+118/token.txt"
+  },
   "sleeptime": 5
 }''')])