X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/24f455da9cb2bf7a3c519912abbc15292a414655..126a8a239853e46cef3d4b7e5acf7620c0bd1f36:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index d489e69897..9982f6ffd5 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -17,6 +17,8 @@ import arvados.keep from .matcher import JsonDiffMatcher from .mock_discovery import get_rootDesc +import ruamel.yaml as yaml + _rootDesc = None def stubs(func): @@ -104,7 +106,7 @@ def stubs(func): 'script_parameters': { 'x': { 'basename': 'blorp.txt', - 'location': 'keep:99999999999999999999999999999994+99/blorp.txt', + 'location': 'keep:99999999999999999999999999999992+99/blorp.txt', 'class': 'File' }, 'y': { @@ -122,10 +124,11 @@ def stubs(func): 'class': 'Directory' }, 'cwl:tool': - '99999999999999999999999999999991+99/wf/submit_wf.cwl' + '99999999999999999999999999999994+99/workflow.cwl#main' }, 'repository': 'arvados', - 'script_version': arvados_cwl.__version__, + 'script_version': 'master', + 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner' } stubs.pipeline_component = stubs.expect_job_spec.copy() @@ -138,16 +141,18 @@ def stubs(func): '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'}}, + 'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999992+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 + 'cwl:tool': '99999999999999999999999999999994+99/workflow.cwl#main', + 'arv:enable_reuse': True, + 'arv:on_error': 'continue' }, 'repository': 'arvados', - 'script_version': arvados_cwl.__version__, + 'script_version': 'master', + 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner', 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'} } @@ -164,6 +169,9 @@ def stubs(func): stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job + with open("tests/wf/submit_wf_packed.cwl") as f: + expect_packed_workflow = yaml.round_trip_load(f) + stubs.expect_container_spec = { 'priority': 1, 'mounts': { @@ -171,22 +179,31 @@ def stubs(func): 'writable': True, 'kind': 'collection' }, - '/var/lib/cwl/workflow': { - 'portable_data_hash': '99999999999999999999999999999991+99', - 'kind': 'collection' + '/var/lib/cwl/workflow.json': { + 'content': expect_packed_workflow, + 'kind': 'json' }, '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' + '/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:99999999999999999999999999999992+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': None, - 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/job/cwl.input.json'], + 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', + '--enable-reuse', '--on-error=continue', + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], 'name': 'submit_wf.cwl', 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, 'output_path': '/var/spool/cwl', @@ -195,7 +212,8 @@ def stubs(func): 'API': True, 'vcpus': 1, 'ram': 1024*1024*1024 - } + }, + "properties": {} } stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz" @@ -215,44 +233,42 @@ def stubs(func): class TestSubmit(unittest.TestCase): + @mock.patch("arvados_cwl.runner.arv_docker_get_image") @mock.patch("time.sleep") @stubs - def test_submit(self, stubs, tm): + def test_submit(self, stubs, tm, arvdock): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( - ["--submit", "--no-wait", "--debug", + ["--submit", "--no-wait", "--api=jobs", "--debug", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) stubs.api.collections().create.assert_has_calls([ mock.call(), - mock.call(body={ + mock.call(body=JsonDiffMatcher({ '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': 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', - 'replication_desired': None, - 'name': 'New collection' - }, ensure_unique_name=True), + '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', + 'replication_desired': None, + 'name': 'submit_tool.cwl dependencies', + }), ensure_unique_name=True), mock.call().execute(num_retries=4), - mock.call(body={ + mock.call(body=JsonDiffMatcher({ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', - 'owner_uuid': None, - 'name': '#', - }, ensure_unique_name=True), - mock.call().execute()]) + 'replication_desired': None, + 'name': 'submit_wf.cwl input', + }), ensure_unique_name=True), + mock.call().execute(num_retries=4)]) + + arvdock.assert_has_calls([ + mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None), + mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None) + ]) expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) stubs.api.pipeline_instances().create.assert_called_with( - body=expect_pipeline) + body=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @@ -262,16 +278,34 @@ class TestSubmit(unittest.TestCase): def test_submit_no_reuse(self, stubs, tm): capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( - ["--submit", "--no-wait", "--debug", "--disable-reuse", + ["--submit", "--no-wait", "--api=jobs", "--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["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False} + + 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_on_error(self, stubs, tm): + capture_stdout = cStringIO.StringIO() + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 0) expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) + expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop" + stubs.api.pipeline_instances().create.assert_called_with( - body=expect_pipeline) + body=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @@ -286,11 +320,11 @@ class TestSubmit(unittest.TestCase): 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) + expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048 + stubs.api.pipeline_instances().create.assert_called_with( - body=expect_pipeline) + body=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @@ -317,11 +351,30 @@ class TestSubmit(unittest.TestCase): 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) + expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name + + 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_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) expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) + expect_pipeline["name"] = "hello job 123" + stubs.api.pipeline_instances().create.assert_called_with( - body=expect_pipeline) + body=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @@ -337,11 +390,11 @@ class TestSubmit(unittest.TestCase): 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) + expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags + stubs.api.pipeline_instances().create.assert_called_with( - body=expect_pipeline) + body=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') @@ -360,7 +413,7 @@ class TestSubmit(unittest.TestCase): 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) + body=JsonDiffMatcher(expect_pipeline)) @stubs def test_submit_container(self, stubs): @@ -376,32 +429,24 @@ class TestSubmit(unittest.TestCase): stubs.api.collections().create.assert_has_calls([ mock.call(), - mock.call(body={ + mock.call(body=JsonDiffMatcher({ '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': 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', - 'name': 'New collection', - 'replication_desired': None, - }, ensure_unique_name=True), + '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', + 'replication_desired': None, + 'name': 'submit_tool.cwl dependencies', + }), ensure_unique_name=True), mock.call().execute(num_retries=4), - mock.call(body={ + mock.call(body=JsonDiffMatcher({ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', - 'owner_uuid': None, - 'name': '#', - }, ensure_unique_name=True), - mock.call().execute()]) + 'replication_desired': None, + 'name': 'submit_wf.cwl input', + }), ensure_unique_name=True), + mock.call().execute(num_retries=4)]) expect_container = copy.deepcopy(stubs.expect_container_spec) 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') @@ -417,11 +462,36 @@ class TestSubmit(unittest.TestCase): 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["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', + '--disable-reuse', '--on-error=continue', + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] + + 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_on_error(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop", + "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("") expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', + '--enable-reuse', '--on-error=stop', + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] + 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') @@ -439,11 +509,14 @@ class TestSubmit(unittest.TestCase): 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) + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', + "--output-name="+output_name, '--enable-reuse', '--on-error=continue', + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] + expect_container["output_name"] = output_name + 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') @@ -461,11 +534,13 @@ class TestSubmit(unittest.TestCase): 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) + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', + "--output-tags="+output_tags, '--enable-reuse', '--on-error=continue', + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] + 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') @@ -481,11 +556,11 @@ class TestSubmit(unittest.TestCase): except: logging.exception("") - stubs.expect_container_spec["runtime_constraints"]["ram"] = 2048*1024*1024 - expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container["runtime_constraints"]["ram"] = 2048*1024*1024 + 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') @@ -531,36 +606,66 @@ class TestSubmit(unittest.TestCase): 'portable_data_hash': '99999999999999999999999999999994+99', 'kind': 'collection' }, - '/var/lib/cwl/job/cwl.input.json': { - 'portable_data_hash': 'e5454f8ca7d5b181e21ecd45841e3373+58/cwl.input.json', - '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', '--enable-reuse', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/job/cwl.input.json'], + 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', + '--enable-reuse', '--on-error=continue', + '/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=expect_container) + 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_jobs_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=jobs", "--debug", + "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 0) + + expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) + expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX" + del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"] + del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"] + expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main" + expect_pipeline["name"] = "expect_arvworkflow.cwl#main" + stubs.api.pipeline_instances().create.assert_called_with( + body=JsonDiffMatcher(expect_pipeline)) + @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()} + stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"} exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -581,9 +686,23 @@ class TestSubmit(unittest.TestCase): }, '/var/lib/cwl/workflow.json': { 'kind': 'json', - 'json': { + 'content': { 'cwlVersion': 'v1.0', '$graph': [ + { + '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': [] + }, { 'inputs': [ { @@ -598,42 +717,99 @@ class TestSubmit(unittest.TestCase): '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/job/cwl.input.json': { - 'portable_data_hash': 'e5454f8ca7d5b181e21ecd45841e3373+58/cwl.input.json', - 'kind': 'collection'} + '/var/lib/cwl/cwl.input.json': { + 'content': { + 'x': 'XxX' + }, + 'kind': 'json' + } }, 'state': 'Committed', 'owner_uuid': None, 'output_path': '/var/spool/cwl', - 'name': 'arvwf:962eh-7fd4e-gkbzl62qqtfig37#main', + 'name': 'a test workflow', 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, - 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/job/cwl.input.json'], + 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', + '--enable-reuse', '--on-error=continue', + '/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=expect_container) + 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("") + + expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container["name"] = "hello container 123" + + 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_job_runner_image(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs: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_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123" + + 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') + + @stubs + def test_submit_container_runner_image(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs: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["container_image"] = "arvados/jobs:123" + + 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') @@ -679,31 +855,17 @@ class TestSubmit(unittest.TestCase): }], "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)) + self.assertEqual("arvados/jobs:"+arvados_cwl.__version__, arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__)) class TestCreateTemplate(unittest.TestCase): - @stubs - def test_create(self, stubs): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - - capture_stdout = cStringIO.StringIO() + existing_template_uuid = "zzzzz-d1hrv-validworkfloyml" - 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_instances().create.refute_called() - stubs.api.jobs().create.refute_called() - - expect_component = copy.deepcopy(stubs.expect_job_spec) + def _adjust_script_params(self, expect_component): expect_component['script_parameters']['x'] = { 'dataclass': 'File', 'required': True, 'type': 'File', - 'value': '99999999999999999999999999999994+99/blorp.txt', + 'value': '99999999999999999999999999999992+99/blorp.txt', } expect_component['script_parameters']['y'] = { 'dataclass': 'Collection', @@ -716,6 +878,26 @@ 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, @@ -730,6 +912,76 @@ 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() @@ -765,6 +1017,39 @@ class TestCreateWorkflow(unittest.TestCase): self.assertEqual(capture_stdout.getvalue(), 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() @@ -807,6 +1092,31 @@ class TestCreateWorkflow(unittest.TestCase): 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": { @@ -817,8 +1127,7 @@ class TestTemplateInputs(unittest.TestCase): }, 'script_parameters': { 'cwl:tool': - '99999999999999999999999999999991+99/' - 'wf/inputs_test.cwl', + '99999999999999999999999999999992+99/workflow.cwl#main', 'optionalFloatInput': None, 'fileInput': { 'type': 'File', @@ -848,7 +1157,8 @@ class TestTemplateInputs(unittest.TestCase): }, }, 'repository': 'arvados', - 'script_version': arvados_cwl.__version__, + 'script_version': 'master', + 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner', }, }, @@ -858,7 +1168,7 @@ 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) @@ -869,7 +1179,7 @@ class TestTemplateInputs(unittest.TestCase): @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) @@ -877,7 +1187,8 @@ class TestTemplateInputs(unittest.TestCase): expect_template = copy.deepcopy(self.expect_template) params = expect_template[ "components"]["inputs_test.cwl"]["script_parameters"] - params["fileInput"]["value"] = '99999999999999999999999999999994+99/blorp.txt' + params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt' + params["cwl:tool"] = '99999999999999999999999999999994+99/workflow.cwl#main' params["floatInput"]["value"] = 1.234 params["boolInput"]["value"] = True