8937: Merge branch 'master' into 8937-arvput-cached-tokens

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

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 2e682830b4c2364ebeefeafa1b179c0f0d551d91..49545a83dc7ac34eea9acc11dc3e022f2839f22c 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -1,3 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 import copy
 import cStringIO
 import functools
@@ -14,7 +18,7 @@ import arvados_cwl
 import arvados_cwl.runner
 import arvados.keep
 
-from .matcher import JsonDiffMatcher
+from .matcher import JsonDiffMatcher, StripYAMLComments
 from .mock_discovery import get_rootDesc
 
 import ruamel.yaml as yaml
@@ -75,7 +79,18 @@ def stubs(func):
                 if uuid in (v["uuid"], v["portable_data_hash"]):
                     return CollectionExecute(v)
 
-        created_collections = {}
+        created_collections = {
+            "99999999999999999999999999999998+99": {
+                "uuid": "",
+                "portable_data_hash": "99999999999999999999999999999998+99",
+                "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
+            },
+            "99999999999999999999999999999994+99": {
+                "uuid": "",
+                "portable_data_hash": "99999999999999999999999999999994+99",
+                "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl"
+            }
+        }
         stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
         stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
 
@@ -138,10 +153,23 @@ def stubs(func):
                     'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
                     'script_parameters': {
                         'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
-                        'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'}},
+                        'x': {"value": {
+                            'basename': 'blorp.txt',
+                            'class': 'File',
+                            'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+                            "nameext": ".txt",
+                            "nameroot": "blorp",
+                            "size": 16
+                        }},
                         'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
                               'listing': [
-                                  {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+                                  {
+                                      'basename': 'renamed.txt',
+                                      'class': 'File', 'location':
+                                      'keep:99999999999999999999999999999998+99/file1.txt',
+                                      "nameext": ".txt",
+                                      "nameroot": "renamed"
+                                  }
                               ]}},
                         'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
                         'arv:enable_reuse': True,
@@ -187,10 +215,25 @@ def stubs(func):
                 '/var/lib/cwl/cwl.input.json': {
                     'kind': 'json',
                     'content': {
-                        'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
-                        'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'},
+                        'y': {
+                            'basename': '99999999999999999999999999999998+99',
+                            'location': 'keep:99999999999999999999999999999998+99',
+                            'class': 'Directory'},
+                        'x': {
+                            'basename': u'blorp.txt',
+                            'class': 'File',
+                            'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+                            "nameext": ".txt",
+                            "nameroot": "blorp",
+                            "size": 16
+                        },
                         'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
-                            {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+                            {'basename': 'renamed.txt',
+                             'class': 'File',
+                             'location': 'keep:99999999999999999999999999999998+99/file1.txt',
+                             "nameext": ".txt",
+                             "nameroot": "renamed"
+                            }
                         ]}
                     },
                     'kind': 'json'
@@ -817,6 +860,31 @@ class TestSubmit(unittest.TestCase):
                          stubs.expect_container_request_uuid + '\n')
 
 
+    @stubs
+    def test_submit_container_project(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+        capture_stdout = cStringIO.StringIO()
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
+                 "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+                capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+            self.assertEqual(exited, 0)
+        except:
+            logging.exception("")
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["owner_uuid"] = project_uuid
+        expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps',
+                                       '--enable-reuse', '--on-error=continue', '--project-uuid='+project_uuid,
+                                       '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+        stubs.api.container_requests().create.assert_called_with(
+            body=JsonDiffMatcher(expect_container))
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_container_request_uuid + '\n')
+
+
     @stubs
     def test_submit_job_runner_image(self, stubs):
         capture_stdout = cStringIO.StringIO()
@@ -1017,7 +1085,8 @@ class TestCreateTemplate(unittest.TestCase):
 
 class TestCreateWorkflow(unittest.TestCase):
     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
-    expect_workflow = open("tests/wf/expect_packed.cwl").read()
+    expect_workflow = StripYAMLComments(
+        open("tests/wf/expect_packed.cwl").read())
 
     @stubs
     def test_create(self, stubs):
@@ -1164,7 +1233,8 @@ class TestCreateWorkflow(unittest.TestCase):
             capture_stdout, sys.stderr, api_client=stubs.api)
         self.assertEqual(exited, 0)
 
-        expect_workflow = open("tests/collection_per_tool/collection_per_tool_packed.cwl").read()
+        toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
+        expect_workflow = StripYAMLComments(open(toolfile).read())
 
         body = {
             "workflow": {