X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/47e42f1129363c2565e69c36ff26ce9c42731fb8..6599088b45103087b4be743fd51a8330e694e57f:/sdk/cwl/tests/test_submit.py?ds=sidebyside diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 6674efb8c4..14ae7b9f8f 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -1,43 +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 json -import logging + +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 = get_rootDesc() + stubs.api.users().current().execute.return_value = { "uuid": stubs.fake_user_uuid, } @@ -60,7 +69,13 @@ def stubs(func): "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"} @@ -83,7 +98,8 @@ def stubs(func): } stubs.expect_job_spec = { 'runtime_constraints': { - 'docker_image': 'arvados/jobs' + 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'min_ram_mb_per_node': 1024 }, 'script_parameters': { 'x': { @@ -110,8 +126,45 @@ def stubs(func): }, 'repository': 'arvados', 'script_version': 'master', + 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner' } + stubs.pipeline_component = stubs.expect_job_spec.copy() + 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__, 'min_ram_mb_per_node': 1024}, + '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': 'master', + 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', + '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, @@ -128,40 +181,56 @@ def stubs(func): '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' + '/var/lib/cwl/cwl.input.json': { + 'kind': 'json', + 'content': { + 'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}, + 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:99999999999999999999999999999994+99/blorp.txt'}, + 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [ + {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'} + ]} + }, + 'kind': 'json' } }, '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', '--no-log-timestamps', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'], 'name': 'submit_wf.cwl', - 'container_image': '99999999999999999999999999999993+99', + 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, 'output_path': '/var/spool/cwl', 'cwd': '/var/spool/cwl', 'runtime_constraints': { 'API': True, 'vcpus': 1, - 'ram': 268435456 - } + 'ram': 1024*1024*1024 + }, + "properties": {} } stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz" 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 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) @@ -173,13 +242,12 @@ 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), @@ -187,21 +255,128 @@ 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_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) + 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=JsonDiffMatcher(expect_pipeline)) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_pipeline_uuid + '\n') + + + @mock.patch("time.sleep") + @stubs + def test_submit_runner_ram(self, stubs, tm): + capture_stdout = cStringIO.StringIO() + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048", + "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"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048 + + expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) + stubs.api.pipeline_instances().create.assert_called_with( + body=JsonDiffMatcher(expect_pipeline)) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_pipeline_uuid + '\n') + + + @mock.patch("time.sleep") + @stubs + def test_submit_invalid_runner_ram(self, stubs, tm): + capture_stdout = cStringIO.StringIO() + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 1) + + @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=JsonDiffMatcher(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_pipeline_name(self, stubs, tm): + capture_stdout = cStringIO.StringIO() + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--debug", "--name=hello job 123", + "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["name"] = "hello job 123" + + 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=JsonDiffMatcher(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( @@ -211,11 +386,10 @@ 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=JsonDiffMatcher(expect_pipeline)) @stubs def test_submit_container(self, stubs): @@ -236,13 +410,12 @@ 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), @@ -250,37 +423,335 @@ 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) + body=JsonDiffMatcher(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', '--no-log-timestamps', + '--disable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'] + + expect_container = copy.deepcopy(stubs.expect_container_spec) + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(expect_container)) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') -class TestCreateTemplate(unittest.TestCase): @stubs - def test_create(self, stubs): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + 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', '--no-log-timestamps', + "--output-name="+output_name, '--enable-reuse', + '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'] + stubs.expect_container_spec["output_name"] = output_name + + expect_container = copy.deepcopy(stubs.expect_container_spec) + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(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', '--no-log-timestamps', + "--output-tags="+output_tags, '--enable-reuse', + '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/cwl.input.json'] + + expect_container = copy.deepcopy(stubs.expect_container_spec) + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(expect_container)) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + @stubs + def test_submit_container_runner_ram(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048", + "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["runtime_constraints"]["ram"] = 2048*1024*1024 + + expect_container = copy.deepcopy(stubs.expect_container_spec) + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(expect_container)) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + @mock.patch("arvados.collection.CollectionReader") + @mock.patch("time.sleep") + @stubs + def test_submit_file_keepref(self, stubs, tm, collectionReader): + capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( - ["--create-template", "--debug", - "--project-uuid", project_uuid, - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + ["--submit", "--no-wait", "--api=containers", "--debug", + "tests/wf/submit_keepref_wf.cwl"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) - stubs.api.pipeline_instances().create.refute_called() - stubs.api.jobs().create.refute_called() - expect_component = copy.deepcopy(stubs.expect_job_spec) + @mock.patch("arvados.collection.CollectionReader") + @mock.patch("time.sleep") + @stubs + def test_submit_keepref(self, stubs, tm, reader): + capture_stdout = cStringIO.StringIO() + + with open("tests/wf/expect_arvworkflow.cwl") as f: + reader().open().__enter__().read.return_value = f.read() + + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", + "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 0) + + expect_container = { + 'priority': 1, + 'mounts': { + '/var/spool/cwl': { + 'writable': True, + 'kind': 'collection' + }, + 'stdout': { + 'path': '/var/spool/cwl/cwl.output.json', + 'kind': 'file' + }, + '/var/lib/cwl/workflow': { + 'portable_data_hash': '99999999999999999999999999999994+99', + 'kind': 'collection' + }, + '/var/lib/cwl/cwl.input.json': { + 'content': { + 'x': 'XxX' + }, + 'kind': 'json' + } + }, 'state': 'Committed', + 'owner_uuid': None, + 'output_path': '/var/spool/cwl', + 'name': 'expect_arvworkflow.cwl#main', + 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', + '--enable-reuse', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'], + 'cwd': '/var/spool/cwl', + 'runtime_constraints': { + 'API': True, + 'vcpus': 1, + 'ram': 1073741824 + }, + "properties": {} + } + + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(expect_container)) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + @mock.patch("time.sleep") + @stubs + def test_submit_arvworkflow(self, stubs, tm): + capture_stdout = cStringIO.StringIO() + + with open("tests/wf/expect_arvworkflow.cwl") as f: + stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"} + + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", + "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 0) + + expect_container = { + 'priority': 1, + 'mounts': { + '/var/spool/cwl': { + 'writable': True, + 'kind': 'collection' + }, + 'stdout': { + 'path': '/var/spool/cwl/cwl.output.json', + 'kind': 'file' + }, + '/var/lib/cwl/workflow.json': { + 'kind': 'json', + 'json': { + 'cwlVersion': 'v1.0', + '$graph': [ + { + 'inputs': [ + { + 'inputBinding': {'position': 1}, + 'type': 'string', + 'id': '#submit_tool.cwl/x'} + ], + 'requirements': [ + {'dockerPull': 'debian:8', 'class': 'DockerRequirement'} + ], + 'id': '#submit_tool.cwl', + 'outputs': [], + 'baseCommand': 'cat', + 'class': 'CommandLineTool' + }, { + 'id': '#main', + 'inputs': [ + {'type': 'string', 'id': '#main/x'} + ], + 'steps': [ + {'in': [{'source': '#main/x', 'id': '#main/step1/x'}], + 'run': '#submit_tool.cwl', + 'id': '#main/step1', + 'out': []} + ], + 'class': 'Workflow', + 'outputs': [] + } + ] + } + }, + '/var/lib/cwl/cwl.input.json': { + 'content': { + 'x': 'XxX' + }, + 'kind': 'json' + } + }, 'state': 'Committed', + 'owner_uuid': None, + 'output_path': '/var/spool/cwl', + 'name': 'a test workflow', + 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', + '--enable-reuse', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], + 'cwd': '/var/spool/cwl', + 'runtime_constraints': { + 'API': True, + 'vcpus': 1, + 'ram': 1073741824 + }, + "properties": { + "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37" + } + } + + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(expect_container)) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + + @stubs + def test_submit_container_name(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123", + "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["name"] = "hello container 123" + + 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): + existing_template_uuid = "zzzzz-d1hrv-validworkfloyml" + + def _adjust_script_params(self, expect_component): expect_component['script_parameters']['x'] = { 'dataclass': 'File', 'required': True, @@ -298,6 +769,26 @@ class TestCreateTemplate(unittest.TestCase): 'required': True, 'type': 'Directory', } + + @stubs + def test_create(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + + capture_stdout = cStringIO.StringIO() + + exited = arvados_cwl.main( + ["--create-workflow", "--debug", + "--api=jobs", + "--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_instances().create.refute_called() + stubs.api.jobs().create.refute_called() + + expect_component = copy.deepcopy(stubs.expect_job_spec) + self._adjust_script_params(expect_component) expect_template = { "components": { "submit_wf.cwl": expect_component, @@ -312,7 +803,80 @@ class TestCreateTemplate(unittest.TestCase): stubs.expect_pipeline_template_uuid + '\n') + @stubs + def test_create_name(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + + capture_stdout = cStringIO.StringIO() + + exited = arvados_cwl.main( + ["--create-workflow", "--debug", + "--project-uuid", project_uuid, + "--api=jobs", + "--name", "testing 123", + "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_instances().create.refute_called() + stubs.api.jobs().create.refute_called() + + expect_component = copy.deepcopy(stubs.expect_job_spec) + self._adjust_script_params(expect_component) + expect_template = { + "components": { + "testing 123": expect_component, + }, + "name": "testing 123", + "owner_uuid": project_uuid, + } + stubs.api.pipeline_templates().create.assert_called_with( + body=JsonDiffMatcher(expect_template), ensure_unique_name=True) + + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_pipeline_template_uuid + '\n') + + + @stubs + def test_update_name(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + + capture_stdout = cStringIO.StringIO() + + exited = arvados_cwl.main( + ["--update-workflow", self.existing_template_uuid, + "--debug", + "--project-uuid", project_uuid, + "--api=jobs", + "--name", "testing 123", + "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_instances().create.refute_called() + stubs.api.jobs().create.refute_called() + + expect_component = copy.deepcopy(stubs.expect_job_spec) + self._adjust_script_params(expect_component) + expect_template = { + "components": { + "testing 123": expect_component, + }, + "name": "testing 123", + "owner_uuid": project_uuid, + } + stubs.api.pipeline_templates().create.refute_called() + stubs.api.pipeline_templates().update.assert_called_with( + body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid) + + self.assertEqual(capture_stdout.getvalue(), + self.existing_template_uuid + '\n') + + 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' @@ -321,6 +885,7 @@ 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) @@ -329,16 +894,13 @@ 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)) @@ -347,12 +909,112 @@ class TestCreateWorkflow(unittest.TestCase): stubs.expect_workflow_uuid + '\n') + @stubs + def test_create_name(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + + capture_stdout = cStringIO.StringIO() + + exited = arvados_cwl.main( + ["--create-workflow", "--debug", + "--api=containers", + "--project-uuid", project_uuid, + "--name", "testing 123", + "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() + + body = { + "workflow": { + "owner_uuid": project_uuid, + "name": "testing 123", + "description": "", + "definition": self.expect_workflow, + } + } + stubs.api.workflows().create.assert_called_with( + body=JsonDiffMatcher(body)) + + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_workflow_uuid + '\n') + + @stubs + def test_incompatible_api(self, stubs): + capture_stderr = cStringIO.StringIO() + logging.getLogger('arvados.cwl-runner').addHandler( + logging.StreamHandler(capture_stderr)) + + exited = arvados_cwl.main( + ["--update-workflow", self.existing_workflow_uuid, + "--api=jobs", + "--debug", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + sys.stderr, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 1) + self.assertRegexpMatches( + capture_stderr.getvalue(), + "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid)) + + @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') + + + @stubs + def test_update_name(self, stubs): + capture_stdout = cStringIO.StringIO() + + exited = arvados_cwl.main( + ["--update-workflow", self.existing_workflow_uuid, + "--debug", "--name", "testing 123", + "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": "testing 123", + "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 = { "components": { "inputs_test.cwl": { 'runtime_constraints': { - 'docker_image': 'arvados/jobs', + 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'min_ram_mb_per_node': 1024 }, 'script_parameters': { 'cwl:tool': @@ -388,6 +1050,7 @@ class TestTemplateInputs(unittest.TestCase): }, 'repository': 'arvados', 'script_version': 'master', + 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner', }, }, @@ -397,29 +1060,23 @@ class TestTemplateInputs(unittest.TestCase): @stubs def test_inputs_empty(self, stubs): exited = arvados_cwl.main( - ["--create-template", "--no-wait", + ["--create-template", "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"], 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): exited = arvados_cwl.main( - ["--create-template", "--no-wait", + ["--create-template", "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"], 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'