X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/25505fc5105bc776ed2d6d898f18f91d6451088b..8668135855b400e7f6047ecacd9cfa27fed723f7:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 432aba21ca..c195b03916 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -1,39 +1,52 @@ -import arvados -import arvados.keep -import arvados.collection -import arvados_cwl import copy import cStringIO import functools import hashlib +import json +import logging import mock import sys 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, KeepClient, keepdocker, *args, **kwargs): + def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs): class Stubs: pass stubs = Stubs() stubs.events = events - stubs.KeepClient = KeepClient stubs.keepdocker = keepdocker + def putstub(p, **kwargs): return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p)) - stubs.KeepClient().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.keepdocker.return_value = True + 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 = get_rootDesc() + stubs.api.users().current().execute.return_value = { "uuid": stubs.fake_user_uuid, } @@ -41,45 +54,164 @@ def stubs(func): 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": "" + }, + { + "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz6", + "portable_data_hash": "99999999999999999999999999999996+99", + "manifest_text": "" + } + ) + stubs.api.collections().get().execute.return_value = { + "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 = { "uuid": stubs.expect_job_uuid, "state": "Queued", } + + stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz" + stubs.api.container_requests().create().execute.return_value = { + "uuid": stubs.expect_container_request_uuid, + "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz", + "state": "Queued" + } + stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz" stubs.api.pipeline_templates().create().execute.return_value = { "uuid": stubs.expect_pipeline_template_uuid, } stubs.expect_job_spec = { 'runtime_constraints': { - 'docker_image': 'arvados/jobs' + 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__ }, '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' }, 'repository': 'arvados', - 'script_version': 'master', + 'script_version': arvados_cwl.__version__, 'script': 'cwl-runner' } + stubs.pipeline_component = stubs.expect_job_spec.copy() + stubs.expect_pipeline_instance = { + 'name': 'submit_wf.cwl', + 'state': 'RunningOnServer', + "components": { + "cwl-runner": { + 'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__}, + 'script_parameters': { + 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}}, + 'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999994+99/blorp.txt'}}, + 'z': {"value": {'basename': 'anonymous', 'class': 'Directory', + 'listing': [ + {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'} + ]}}, + 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl', + 'arv:enable_reuse': True + }, + 'repository': 'arvados', + 'script_version': arvados_cwl.__version__, + 'script': 'cwl-runner', + 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'} + } + } + } + stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance) + stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz" + stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid + stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create) + stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = { + "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", + "state": "Queued" + } + stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create + stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job + + stubs.expect_container_spec = { + 'priority': 1, + 'mounts': { + '/var/spool/cwl': { + 'writable': True, + 'kind': 'collection' + }, + '/var/lib/cwl/workflow': { + 'portable_data_hash': '99999999999999999999999999999991+99', + 'kind': 'collection' + }, + 'stdout': { + 'path': '/var/spool/cwl/cwl.output.json', + 'kind': 'file' + }, + '/var/lib/cwl/job/cwl.input.json': { + 'portable_data_hash': 'd20d7cddd1984f105dd3702c7f125afb+60/cwl.input.json', + 'kind': 'collection' + } + }, + 'state': 'Committed', + 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + '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', + 'cwd': '/var/spool/cwl', + 'runtime_constraints': { + 'API': True, + 'vcpus': 1, + '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 class TestSubmit(unittest.TestCase): + @mock.patch("time.sleep") @stubs - def test_submit(self, stubs): + def test_submit(self, stubs, tm): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( - ["--submit", "--no-wait", + ["--submit", "--no-wait", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) @@ -88,13 +220,20 @@ class TestSubmit(unittest.TestCase): mock.call(), mock.call(body={ 'manifest_text': - './tool 84ec4df683711de31b782505389a8843+429 ' - '0:16:blub.txt 16:413:submit_tool.cwl\n./wf ' - '81d977a245a41b8e79859fbe00623fd0+344 0:344: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', @@ -103,16 +242,36 @@ class TestSubmit(unittest.TestCase): }, ensure_unique_name=True), mock.call().execute()]) - expect_job = copy.deepcopy(stubs.expect_job_spec) - expect_job["owner_uuid"] = stubs.fake_user_uuid - stubs.api.jobs().create.assert_called_with( - body=expect_job, - find_or_create=True) + 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_job_uuid + '\n') + stubs.expect_pipeline_uuid + '\n') + + @mock.patch("time.sleep") @stubs - def test_submit_with_project_uuid(self, 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) + 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_with_project_uuid(self, stubs, tm): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' exited = arvados_cwl.main( @@ -122,12 +281,119 @@ class TestSubmit(unittest.TestCase): sys.stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) - expect_body = copy.deepcopy(stubs.expect_job_spec) - expect_body["owner_uuid"] = project_uuid - stubs.api.jobs().create.assert_called_with( - body=expect_body, - find_or_create=True) + expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) + expect_pipeline["owner_uuid"] = project_uuid + stubs.api.pipeline_instances().create.assert_called_with( + body=expect_pipeline) + @stubs + def test_submit_container(self, stubs): + capture_stdout = cStringIO.StringIO() + 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 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', + 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz', + '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) + 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') + + @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 @@ -137,7 +403,7 @@ class TestCreateTemplate(unittest.TestCase): 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) @@ -151,7 +417,18 @@ class TestCreateTemplate(unittest.TestCase): '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": { @@ -161,18 +438,53 @@ class TestCreateTemplate(unittest.TestCase): "owner_uuid": project_uuid, } stubs.api.pipeline_templates().create.assert_called_with( - body=JsonDiffMatcher(expect_template)) + body=JsonDiffMatcher(expect_template), ensure_unique_name=True) self.assertEqual(capture_stdout.getvalue(), 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": { "inputs_test.cwl": { 'runtime_constraints': { - 'docker_image': 'arvados/jobs', + 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, }, 'script_parameters': { 'cwl:tool': @@ -207,7 +519,7 @@ class TestTemplateInputs(unittest.TestCase): }, }, 'repository': 'arvados', - 'script_version': 'master', + 'script_version': arvados_cwl.__version__, 'script': 'cwl-runner', }, }, @@ -226,7 +538,7 @@ class TestTemplateInputs(unittest.TestCase): expect_template["owner_uuid"] = stubs.fake_user_uuid stubs.api.pipeline_templates().create.assert_called_with( - body=JsonDiffMatcher(expect_template)) + body=JsonDiffMatcher(expect_template), ensure_unique_name=True) @stubs def test_inputs(self, stubs): @@ -242,9 +554,9 @@ class TestTemplateInputs(unittest.TestCase): 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 stubs.api.pipeline_templates().create.assert_called_with( - body=JsonDiffMatcher(expect_template)) + body=JsonDiffMatcher(expect_template), ensure_unique_name=True)