X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/779c5400a4f376489f4abc8564f890f309ae3f20..47e42f1129363c2565e69c36ff26ce9c42731fb8:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 2dff3e8f9d..6674efb8c4 100644 --- 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": {