X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/670b4ba238d93910ff087794d359da0d5ac469fa..a4e81f561cce966074a72ff6219826a89152451a:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 7faef6992c..95ccd9e8af 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -11,35 +11,42 @@ import unittest import arvados import arvados.collection import arvados_cwl +import arvados_cwl.runner import arvados.keep from .matcher import JsonDiffMatcher +from .mock_discovery import get_rootDesc +_rootDesc = None def stubs(func): @functools.wraps(func) @mock.patch("arvados.commands.keepdocker.list_images_in_arv") @mock.patch("arvados.collection.KeepClient") + @mock.patch("arvados.keep.KeepClient") @mock.patch("arvados.events.subscribe") - def wrapped(self, events, keep_client, keepdocker, *args, **kwargs): + def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs): class Stubs: pass stubs = Stubs() stubs.events = events stubs.keepdocker = keepdocker - stubs.keep_client = keep_client + def putstub(p, **kwargs): return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p)) - stubs.keep_client().put.side_effect = putstub - stubs.keep_client.put.side_effect = putstub + keep_client1().put.side_effect = putstub + keep_client1.put.side_effect = putstub + keep_client2().put.side_effect = putstub + keep_client2.put.side_effect = putstub + stubs.keep_client = keep_client2 stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz" - stubs.api = mock.MagicMock() - stubs.api._rootDesc = arvados.api('v1')._rootDesc + stubs.api._rootDesc = get_rootDesc() + stubs.api.users().current().execute.return_value = { "uuid": stubs.fake_user_uuid, } @@ -124,6 +131,7 @@ def stubs(func): stubs.expect_pipeline_instance = { 'name': 'submit_wf.cwl', 'state': 'RunningOnServer', + 'owner_uuid': None, "components": { "cwl-runner": { 'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__}, @@ -134,7 +142,8 @@ def stubs(func): 'listing': [ {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'} ]}}, - 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl' + 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl', + 'arv:enable_reuse': True }, 'repository': 'arvados', 'script_version': arvados_cwl.__version__, @@ -175,8 +184,8 @@ def stubs(func): } }, 'state': 'Committed', - 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', - 'command': ['arvados-cwl-runner', '--local', '--api=containers', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'], + 'owner_uuid': None, + 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'], 'name': 'submit_wf.cwl', 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, 'output_path': '/var/spool/cwl', @@ -192,6 +201,13 @@ def stubs(func): stubs.api.workflows().create().execute.return_value = { "uuid": stubs.expect_workflow_uuid, } + def update_mock(**kwargs): + stubs.updated_uuid = kwargs.get('uuid') + return mock.DEFAULT + stubs.api.workflows().update.side_effect = update_mock + stubs.api.workflows().update().execute.side_effect = lambda **kwargs: { + "uuid": stubs.updated_uuid, + } return func(self, stubs, *args, **kwargs) return wrapped @@ -215,13 +231,12 @@ class TestSubmit(unittest.TestCase): './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', + 'owner_uuid': None, '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), @@ -229,13 +244,71 @@ class TestSubmit(unittest.TestCase): mock.call(body={ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', - 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + 'owner_uuid': None, 'name': '#', }, ensure_unique_name=True), mock.call().execute()]) expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) - expect_pipeline["owner_uuid"] = stubs.fake_user_uuid + stubs.api.pipeline_instances().create.assert_called_with( + body=expect_pipeline) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_pipeline_uuid + '\n') + + + @mock.patch("time.sleep") + @stubs + def test_submit_no_reuse(self, stubs, tm): + capture_stdout = cStringIO.StringIO() + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--debug", "--disable-reuse", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 0) + + stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False} + + expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) + stubs.api.pipeline_instances().create.assert_called_with( + body=expect_pipeline) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_pipeline_uuid + '\n') + + @mock.patch("time.sleep") + @stubs + def test_submit_output_name(self, stubs, tm): + output_name = "test_output_name" + + capture_stdout = cStringIO.StringIO() + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--debug", "--output-name", output_name, + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 0) + + stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name + + expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) + stubs.api.pipeline_instances().create.assert_called_with( + body=expect_pipeline) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_pipeline_uuid + '\n') + + @mock.patch("time.sleep") + @stubs + def test_submit_output_tags(self, stubs, tm): + output_tags = "tag0,tag1,tag2" + + capture_stdout = cStringIO.StringIO() + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--debug", "--output-tags", output_tags, + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 0) + + stubs.expect_pipeline_instance["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags + + expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) stubs.api.pipeline_instances().create.assert_called_with( body=expect_pipeline) self.assertEqual(capture_stdout.getvalue(), @@ -277,13 +350,12 @@ class TestSubmit(unittest.TestCase): './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', + 'owner_uuid': None, '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), @@ -291,18 +363,123 @@ class TestSubmit(unittest.TestCase): mock.call(body={ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', - 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + 'owner_uuid': None, 'name': '#', }, ensure_unique_name=True), mock.call().execute()]) expect_container = copy.deepcopy(stubs.expect_container_spec) - expect_container["owner_uuid"] = stubs.fake_user_uuid stubs.api.container_requests().create.assert_called_with( body=expect_container) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') + @stubs + def test_submit_container_no_reuse(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse", + "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.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'] + + expect_container = copy.deepcopy(stubs.expect_container_spec) + stubs.api.container_requests().create.assert_called_with( + body=expect_container) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + @stubs + def test_submit_container_output_name(self, stubs): + output_name = "test_output_name" + + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name, + "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.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-name="+output_name, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'] + + expect_container = copy.deepcopy(stubs.expect_container_spec) + stubs.api.container_requests().create.assert_called_with( + body=expect_container) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + @stubs + def test_submit_container_output_tags(self, stubs): + output_tags = "tag0,tag1,tag2" + + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags, + "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.expect_container_spec["command"] = ['arvados-cwl-runner', '--local', '--api=containers', "--output-tags="+output_tags, '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'] + + expect_container = copy.deepcopy(stubs.expect_container_spec) + stubs.api.container_requests().create.assert_called_with( + body=expect_container) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + @mock.patch("arvados.commands.keepdocker.find_one_image_hash") + @mock.patch("cwltool.docker.get_image") + @mock.patch("arvados.api") + def test_arvados_jobs_image(self, api, get_image, find_one_image_hash): + arvrunner = mock.MagicMock() + arvrunner.project_uuid = "" + api.return_value = mock.MagicMock() + arvrunner.api = api.return_value + arvrunner.api.links().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0}, + {"items": [], "items_available": 0, "offset": 0}, + {"items": [], "items_available": 0, "offset": 0}, + {"items": [{"created_at": "", + "head_uuid": "", + "link_class": "docker_image_hash", + "name": "123456", + "owner_uuid": "", + "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}, + {"items": [], "items_available": 0, "offset": 0}, + {"items": [{"created_at": "", + "head_uuid": "", + "link_class": "docker_image_repo+tag", + "name": "arvados/jobs:"+arvados_cwl.__version__, + "owner_uuid": "", + "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}, + {"items": [{"created_at": "", + "head_uuid": "", + "link_class": "docker_image_hash", + "name": "123456", + "owner_uuid": "", + "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0} , + ) + find_one_image_hash.return_value = "123456" + + arvrunner.api.collections().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0}, + {"items": [{"uuid": "", + "owner_uuid": "", + "manifest_text": "", + "properties": "" + }], "items_available": 1, "offset": 0}, + {"items": [{"uuid": ""}], "items_available": 1, "offset": 0}) + arvrunner.api.collections().create().execute.return_value = {"uuid": ""} + self.assertEqual("arvados/jobs:"+arvados_cwl.__version__, arvados_cwl.runner.arvados_jobs_image(arvrunner)) class TestCreateTemplate(unittest.TestCase): @stubs @@ -312,7 +489,7 @@ class TestCreateTemplate(unittest.TestCase): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( - ["--create-template", "--debug", + ["--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) @@ -354,6 +531,9 @@ class TestCreateTemplate(unittest.TestCase): class TestCreateWorkflow(unittest.TestCase): + existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml" + expect_workflow = open("tests/wf/expect_packed.cwl").read() + @stubs def test_create(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' @@ -362,6 +542,7 @@ class TestCreateWorkflow(unittest.TestCase): exited = arvados_cwl.main( ["--create-workflow", "--debug", + "--api=containers", "--project-uuid", project_uuid, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) @@ -370,16 +551,13 @@ class TestCreateWorkflow(unittest.TestCase): 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 - } + "definition": self.expect_workflow, + } } stubs.api.workflows().create.assert_called_with( body=JsonDiffMatcher(body)) @@ -387,6 +565,42 @@ class TestCreateWorkflow(unittest.TestCase): self.assertEqual(capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') + @stubs + def test_incompatible_api(self, stubs): + capture_stdout = cStringIO.StringIO() + + exited = arvados_cwl.main( + ["--update-workflow", self.existing_workflow_uuid, + "--api=jobs", + "--debug", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 1) + + @stubs + def test_update(self, stubs): + capture_stdout = cStringIO.StringIO() + + exited = arvados_cwl.main( + ["--update-workflow", self.existing_workflow_uuid, + "--debug", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 0) + + body = { + "workflow": { + "name": "submit_wf.cwl", + "description": "", + "definition": self.expect_workflow, + } + } + stubs.api.workflows().update.assert_called_with( + uuid=self.existing_workflow_uuid, + body=JsonDiffMatcher(body)) + self.assertEqual(capture_stdout.getvalue(), + self.existing_workflow_uuid + '\n') + class TestTemplateInputs(unittest.TestCase): expect_template = { @@ -443,11 +657,8 @@ class TestTemplateInputs(unittest.TestCase): cStringIO.StringIO(), sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) - expect_template = copy.deepcopy(self.expect_template) - expect_template["owner_uuid"] = stubs.fake_user_uuid - stubs.api.pipeline_templates().create.assert_called_with( - body=JsonDiffMatcher(expect_template), ensure_unique_name=True) + body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True) @stubs def test_inputs(self, stubs): @@ -457,10 +668,7 @@ class TestTemplateInputs(unittest.TestCase): cStringIO.StringIO(), sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) - self.expect_template["owner_uuid"] = stubs.fake_user_uuid - expect_template = copy.deepcopy(self.expect_template) - expect_template["owner_uuid"] = stubs.fake_user_uuid params = expect_template[ "components"]["inputs_test.cwl"]["script_parameters"] params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt'