import mock
import sys
import unittest
+import json
+import logging
from .matcher import JsonDiffMatcher
@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,
stubs.api.collections().create().execute.side_effect = ({
"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1",
"portable_data_hash": "99999999999999999999999999999991+99",
+ "manifest_text": ""
}, {
"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2",
"portable_data_hash": "99999999999999999999999999999992+99",
+ "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"
},
{
"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4",
"portable_data_hash": "99999999999999999999999999999994+99",
"manifest_text": ""
- })
+ },
+ {
+ "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz5",
+ "portable_data_hash": "99999999999999999999999999999995+99",
+ "manifest_text": ""
+ } )
stubs.api.collections().get().execute.return_value = {
- "portable_data_hash": "99999999999999999999999999999993+99"}
+ "portable_data_hash": "99999999999999999999999999999993+99", "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"}
stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
stubs.api.jobs().create().execute.return_value = {
},
'script_parameters': {
'x': {
- 'path': '99999999999999999999999999999992+99/blorp.txt',
+ 'basename': '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'
},
'kind': 'file'
},
'/var/lib/cwl/job/cwl.input.json': {
- 'portable_data_hash': '33be5c865fe12e1e4788d2f1bc627f7a+60/cwl.input.json',
+ 'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json',
'kind': 'collection'
}
},
'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
mock.call(),
mock.call(body={
'manifest_text':
- './tool a3954c369b8924d40547ec8cf5f6a7f4+449 '
- '0:16:blub.txt 16:433:submit_tool.cwl\n./wf '
- 'e046cace0b1a0a6ee645f6ea8688f7e2+364 0:364:submit_wf.cwl\n',
+ './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
+ '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
+ 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
'name': 'submit_wf.cwl',
}, ensure_unique_name=True),
mock.call().execute(),
+ mock.call(body={'manifest_text': '. d41d8cd98f00b204e9800998ecf8427e+0 '
+ '0:0:blub.txt 0:0:submit_tool.cwl\n',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'replication_desired': None,
+ 'name': 'New collection'
+ }, ensure_unique_name=True),
+ mock.call().execute(num_retries=4),
mock.call(body={
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
@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(),
mock.call(body={
'manifest_text':
- './tool a3954c369b8924d40547ec8cf5f6a7f4+449 '
- '0:16:blub.txt 16:433:submit_tool.cwl\n./wf '
- 'e046cace0b1a0a6ee645f6ea8688f7e2+364 0:364:submit_wf.cwl\n',
+ './tool d51232d96b6116d964a69bfb7e0c73bf+450 '
+ '0:16:blub.txt 16:434:submit_tool.cwl\n./wf '
+ 'cc2ffb940e60adf1b2b282c67587e43d+413 0:413:submit_wf.cwl\n',
'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
'name': 'submit_wf.cwl',
}, ensure_unique_name=True),
mock.call().execute(),
+ 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',
+ 'replication_desired': None,
+ }, ensure_unique_name=True),
+ mock.call().execute(num_retries=4),
mock.call(body={
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--create-template", "--no-wait",
+ ["--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)
'dataclass': 'File',
'required': True,
'type': 'File',
- 'value': '99999999999999999999999999999992+99/blorp.txt',
+ '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": {
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": {
expect_template["owner_uuid"] = stubs.fake_user_uuid
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
- params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt'
+ params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'
params["floatInput"]["value"] = 1.234
params["boolInput"]["value"] = True
projects / arvados.git / blobdiff