Merge branch '8018-container-retry' closes #8018

[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 2dff3e8f9dbe422a7ca6e95037384cc4618c920b..6674efb8c4f75c2391160a702588ea2354e377a3 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -9,6 +9,8 @@ import hashlib
 import mock
 import sys
 import unittest
+import json
+import logging
 
 from .matcher import JsonDiffMatcher
 
@@ -18,21 +20,23 @@ def stubs(func):
     @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
     @mock.patch("arvados.collection.KeepClient")
     @mock.patch("arvados.events.subscribe")
-    def wrapped(self, events, KeepClient, keepdocker, *args, **kwargs):
+    def wrapped(self, events, keep_client, keepdocker, *args, **kwargs):
         class Stubs:
             pass
         stubs = Stubs()
         stubs.events = events
-        stubs.KeepClient = KeepClient
         stubs.keepdocker = keepdocker
+        stubs.keep_client = keep_client
 
         def putstub(p, **kwargs):
             return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p))
-        stubs.KeepClient().put.side_effect = putstub
+        stubs.keep_client().put.side_effect = putstub
+        stubs.keep_client.put.side_effect = putstub
 
         stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
         stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
 
+
         stubs.api = mock.MagicMock()
         stubs.api.users().current().execute.return_value = {
             "uuid": stubs.fake_user_uuid,
@@ -84,9 +88,23 @@ def stubs(func):
             'script_parameters': {
                 'x': {
                     'basename': 'blorp.txt',
-                    'location': '99999999999999999999999999999994+99/blorp.txt',
+                    'location': 'keep:99999999999999999999999999999994+99/blorp.txt',
                     'class': 'File'
                 },
+                'y': {
+                    'basename': '99999999999999999999999999999998+99',
+                    'location': 'keep:99999999999999999999999999999998+99',
+                    'class': 'Directory'
+                },
+                'z': {
+                    'basename': 'anonymous',
+                    "listing": [{
+                        "basename": "renamed.txt",
+                        "class": "File",
+                        "location": "keep:99999999999999999999999999999998+99/file1.txt"
+                    }],
+                    'class': 'Directory'
+                },
                 'cwl:tool':
                 '99999999999999999999999999999991+99/wf/submit_wf.cwl'
             },
@@ -111,7 +129,7 @@ def stubs(func):
                     'kind': 'file'
                 },
                 '/var/lib/cwl/job/cwl.input.json': {
-                    'portable_data_hash': '765fda0d9897729ff467a4609879c00a+60/cwl.input.json',
+                    'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json',
                     'kind': 'collection'
                 }
             },
@@ -128,6 +146,12 @@ def stubs(func):
                 'ram': 268435456
             }
         }
+
+        stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
+        stubs.api.workflows().create().execute.return_value = {
+            "uuid": stubs.expect_workflow_uuid,
+        }
+
         return func(self, stubs, *args, **kwargs)
     return wrapped
 
@@ -148,7 +172,7 @@ class TestSubmit(unittest.TestCase):
                 'manifest_text':
                 './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
                 '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
-                '4d31c5fefd087faf67ca8db0111af36c+353 0:353:submit_wf.cwl\n',
+                'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
                 'name': 'submit_wf.cwl',
             }, ensure_unique_name=True),
@@ -156,8 +180,9 @@ class TestSubmit(unittest.TestCase):
             mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
                             '0:0:blub.txt 0:0:submit_tool.cwl\n',
                             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
-                            'name': 'New collection'},
-                      ensure_unique_name=True),
+                            'replication_desired': None,
+                            'name': 'New collection'
+            }, ensure_unique_name=True),
             mock.call().execute(num_retries=4),
             mock.call(body={
                 'manifest_text':
@@ -195,11 +220,14 @@ class TestSubmit(unittest.TestCase):
     @stubs
     def test_submit_container(self, stubs):
         capture_stdout = cStringIO.StringIO()
-        exited = arvados_cwl.main(
-            ["--submit", "--no-wait", "--api=containers", "--debug",
-             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
-            capture_stdout, sys.stderr, api_client=stubs.api)
-        self.assertEqual(exited, 0)
+        try:
+            exited = arvados_cwl.main(
+                ["--submit", "--no-wait", "--api=containers", "--debug",
+                 "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("")
 
         stubs.api.collections().create.assert_has_calls([
             mock.call(),
@@ -207,7 +235,7 @@ class TestSubmit(unittest.TestCase):
                 'manifest_text':
                 './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
                 '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
-                '4d31c5fefd087faf67ca8db0111af36c+353 0:353:submit_wf.cwl\n',
+                'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
                 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
                 'name': 'submit_wf.cwl',
             }, ensure_unique_name=True),
@@ -215,8 +243,9 @@ class TestSubmit(unittest.TestCase):
             mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
                             '0:0:blub.txt 0:0:submit_tool.cwl\n',
                             'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
-                            'name': 'New collection'},
-                      ensure_unique_name=True),
+                            'name': 'New collection',
+                            'replication_desired': None,
+            }, ensure_unique_name=True),
             mock.call().execute(num_retries=4),
             mock.call(body={
                 'manifest_text':
@@ -242,7 +271,7 @@ class TestCreateTemplate(unittest.TestCase):
         capture_stdout = cStringIO.StringIO()
 
         exited = arvados_cwl.main(
-            ["--create-template", "--no-wait", "--debug",
+            ["--create-template", "--debug",
              "--project-uuid", project_uuid,
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             capture_stdout, sys.stderr, api_client=stubs.api)
@@ -258,6 +287,17 @@ class TestCreateTemplate(unittest.TestCase):
             'type': 'File',
             'value': '99999999999999999999999999999994+99/blorp.txt',
         }
+        expect_component['script_parameters']['y'] = {
+            'dataclass': 'Collection',
+            'required': True,
+            'type': 'Directory',
+            'value': '99999999999999999999999999999998+99',
+        }
+        expect_component['script_parameters']['z'] = {
+            'dataclass': 'Collection',
+            'required': True,
+            'type': 'Directory',
+        }
         expect_template = {
             "components": {
                 "submit_wf.cwl": expect_component,
@@ -272,6 +312,41 @@ class TestCreateTemplate(unittest.TestCase):
                          stubs.expect_pipeline_template_uuid + '\n')
 
 
+class TestCreateWorkflow(unittest.TestCase):
+    @stubs
+    def test_create(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+        capture_stdout = cStringIO.StringIO()
+
+        exited = arvados_cwl.main(
+            ["--create-workflow", "--debug",
+             "--project-uuid", project_uuid,
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
+        stubs.api.pipeline_templates().create.refute_called()
+        stubs.api.container_requests().create.refute_called()
+
+        with open("tests/wf/expect_packed.cwl") as f:
+            expect_workflow = f.read()
+
+        body = {
+            "workflow": {
+                "owner_uuid": project_uuid,
+                "name": "submit_wf.cwl",
+                "description": "",
+                "definition": expect_workflow
+                }
+        }
+        stubs.api.workflows().create.assert_called_with(
+            body=JsonDiffMatcher(body))
+
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_workflow_uuid + '\n')
+
+
 class TestTemplateInputs(unittest.TestCase):
     expect_template = {
         "components": {