X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/af17604c5a93830380fb50db93ce543926c116cf..8352a6863cdcc2794108a71fd5b64e7b75f9dd20:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 9cabea0794..1b892a9836 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -15,6 +15,7 @@ import unittest import arvados import arvados.collection import arvados_cwl +import arvados_cwl.executor import arvados_cwl.runner import arvados.keep @@ -46,8 +47,18 @@ def stubs(func): keep_client2.put.side_effect = putstub stubs.keep_client = keep_client2 - stubs.keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")] + stubs.docker_images = { + "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", "")], + "debian:8": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")], + "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", "")], + "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", "")], + } + def kd(a, b, image_name=None, image_tag=None): + return stubs.docker_images.get("%s:%s" % (image_name, image_tag), []) + stubs.keepdocker.side_effect = kd + stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz" + stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz" stubs.api = mock.MagicMock() stubs.api._rootDesc = get_rootDesc() @@ -56,6 +67,9 @@ def stubs(func): "uuid": stubs.fake_user_uuid, } stubs.api.collections().list().execute.return_value = {"items": []} + stubs.api.containers().current().execute.return_value = { + "uuid": stubs.fake_container_uuid, + } class CollectionExecute(object): def __init__(self, exe): @@ -65,7 +79,7 @@ def stubs(func): def collection_createstub(created_collections, body, ensure_unique_name=None): mt = body["manifest_text"] - uuid = "zzzzz-4zz18-zzzzzzzzzzzzzz%d" % len(created_collections) + uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections) pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt)) created_collections[uuid] = { "uuid": uuid, @@ -89,6 +103,26 @@ def stubs(func): "uuid": "", "portable_data_hash": "99999999999999999999999999999994+99", "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl" + }, + "zzzzz-4zz18-zzzzzzzzzzzzzd3": { + "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd3", + "portable_data_hash": "999999999999999999999999999999d3+99", + "manifest_text": "" + }, + "zzzzz-4zz18-zzzzzzzzzzzzzd4": { + "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd4", + "portable_data_hash": "999999999999999999999999999999d4+99", + "manifest_text": "" + }, + "zzzzz-4zz18-zzzzzzzzzzzzzd5": { + "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd5", + "portable_data_hash": "999999999999999999999999999999d5+99", + "manifest_text": "" + }, + "zzzzz-4zz18-zzzzzzzzzzzzzd6": { + "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzd6", + "portable_data_hash": "999999999999999999999999999999d6+99", + "manifest_text": "" } } stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections) @@ -113,7 +147,7 @@ def stubs(func): } stubs.expect_job_spec = { 'runtime_constraints': { - 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024 }, 'script_parameters': { @@ -132,11 +166,12 @@ def stubs(func): "listing": [{ "basename": "renamed.txt", "class": "File", - "location": "keep:99999999999999999999999999999998+99/file1.txt" + "location": "keep:99999999999999999999999999999998+99/file1.txt", + "size": 0 }], 'class': 'Directory' }, - 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main' + 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main' }, 'repository': 'arvados', 'script_version': 'master', @@ -150,7 +185,7 @@ def stubs(func): 'owner_uuid': None, "components": { "cwl-runner": { - 'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024}, + 'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024}, 'script_parameters': { 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}}, 'x': {"value": { @@ -164,10 +199,12 @@ def stubs(func): { 'basename': 'renamed.txt', 'class': 'File', 'location': - 'keep:99999999999999999999999999999998+99/file1.txt' + 'keep:99999999999999999999999999999998+99/file1.txt', + 'size': 0 } ]}}, - 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main', + 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main', + 'arv:debug': True, 'arv:enable_reuse': True, 'arv:on_error': 'continue' }, @@ -194,7 +231,7 @@ def stubs(func): expect_packed_workflow = yaml.round_trip_load(f) stubs.expect_container_spec = { - 'priority': 1, + 'priority': 500, 'mounts': { '/var/spool/cwl': { 'writable': True, @@ -224,20 +261,23 @@ def stubs(func): 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [ {'basename': 'renamed.txt', 'class': 'File', - 'location': 'keep:99999999999999999999999999999998+99/file1.txt' + 'location': 'keep:99999999999999999999999999999998+99/file1.txt', + 'size': 0 } ]} }, 'kind': 'json' } }, + 'secret_mounts': {}, 'state': 'Committed', - 'owner_uuid': None, - 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', - '--enable-reuse', '--on-error=continue', + 'command': ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--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__, + 'container_image': '999999999999999999999999999999d3+99', 'output_path': '/var/spool/cwl', 'cwd': '/var/spool/cwl', 'runtime_constraints': { @@ -246,7 +286,8 @@ def stubs(func): 'ram': 1024*1024*1024 }, 'use_existing': True, - 'properties': {} + 'properties': {}, + 'secret_mounts': {} } stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz" @@ -266,10 +307,17 @@ def stubs(func): class TestSubmit(unittest.TestCase): - @mock.patch("arvados_cwl.runner.arv_docker_get_image") + @mock.patch("arvados_cwl.arvdocker.arv_docker_get_image") @mock.patch("time.sleep") @stubs def test_submit(self, stubs, tm, arvdock): + def get_image(api_client, dockerRequirement, pull_image, project_uuid): + if dockerRequirement["dockerPull"] == 'arvados/jobs:'+arvados_cwl.__version__: + return '999999999999999999999999999999d3+99' + elif dockerRequirement["dockerPull"] == "debian:8": + return '999999999999999999999999999999d4+99' + arvdock.side_effect = get_image + capture_stdout = cStringIO.StringIO() exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=jobs", "--debug", @@ -282,23 +330,24 @@ class TestSubmit(unittest.TestCase): 'manifest_text': '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', 'replication_desired': None, - 'name': 'submit_tool.cwl dependencies', - }), ensure_unique_name=True), + 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', + }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'replication_desired': None, - 'name': 'submit_wf.cwl input', - }), ensure_unique_name=True), + 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', + }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': - '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n', + ". 68089141fbf7e020ac90a9d6a575bc8f+1312 0:1312:workflow.cwl\n", 'replication_desired': None, 'name': 'submit_wf.cwl', }), ensure_unique_name=True) ]) arvdock.assert_has_calls([ mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None), + mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8", 'http://arvados.org/cwl#dockerCollectionPDH': '999999999999999999999999999999d4+99'}, True, None), mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None) ]) @@ -328,6 +377,15 @@ class TestSubmit(unittest.TestCase): self.assertEqual(capture_stdout.getvalue(), stubs.expect_pipeline_uuid + '\n') + @stubs + def test_error_when_multiple_storage_classes_specified(self, stubs): + storage_classes = "foo,bar" + exited = arvados_cwl.main( + ["--debug", "--storage-classes", storage_classes, + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + sys.stdin, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 1) + @mock.patch("time.sleep") @stubs def test_submit_on_error(self, stubs, tm): @@ -441,7 +499,7 @@ class TestSubmit(unittest.TestCase): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' exited = arvados_cwl.main( - ["--submit", "--no-wait", + ["--submit", "--no-wait", "--debug", "--project-uuid", project_uuid, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], sys.stdout, sys.stderr, api_client=stubs.api) @@ -469,14 +527,14 @@ class TestSubmit(unittest.TestCase): 'manifest_text': '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', 'replication_desired': None, - 'name': 'submit_tool.cwl dependencies', - }), ensure_unique_name=True), + 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', + }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'replication_desired': None, - 'name': 'submit_wf.cwl input', - }), ensure_unique_name=True)]) + 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', + }), ensure_unique_name=False)]) expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( @@ -498,8 +556,10 @@ class TestSubmit(unittest.TestCase): 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', + 'arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--disable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] expect_container["use_existing"] = False @@ -521,8 +581,10 @@ class TestSubmit(unittest.TestCase): 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', + 'arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--disable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] expect_container["use_existing"] = False expect_container["name"] = "submit_wf_no_reuse.cwl" @@ -556,9 +618,11 @@ class TestSubmit(unittest.TestCase): 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'] + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=stop', + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) @@ -580,9 +644,12 @@ class TestSubmit(unittest.TestCase): logging.exception("") 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["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', + "--output-name="+output_name, '--debug', '--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( @@ -590,6 +657,72 @@ class TestSubmit(unittest.TestCase): self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') + @stubs + def test_submit_storage_classes(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo", + "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', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', "--debug", + "--storage-classes=foo", '--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') + + @mock.patch("arvados_cwl.task_queue.TaskQueue") + @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") + @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None)) + @stubs + def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq): + def set_final_output(job_order, output_callback, runtimeContext): + output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") + return [] + job.side_effect = set_final_output + + try: + exited = arvados_cwl.main( + ["--debug", "--local", "--storage-classes=foo", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 0) + except: + logging.exception("") + + make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') + + @mock.patch("arvados_cwl.task_queue.TaskQueue") + @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") + @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None)) + @stubs + def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq): + def set_final_output(job_order, output_callback, runtimeContext): + output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") + return [] + job.side_effect = set_final_output + + try: + exited = arvados_cwl.main( + ["--debug", "--local", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 0) + except: + logging.exception("") + + make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') @stubs def test_submit_container_output_ttl(self, stubs): @@ -604,8 +737,10 @@ class TestSubmit(unittest.TestCase): 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=continue', + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=continue', "--intermediate-output-ttl=3600", '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -627,8 +762,10 @@ class TestSubmit(unittest.TestCase): 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=continue', + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=continue', "--trash-intermediate", '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -652,9 +789,12 @@ class TestSubmit(unittest.TestCase): logging.exception("") 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'] + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', + "--output-tags="+output_tags, '--debug', '--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)) @@ -686,6 +826,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_file_keepref(self, stubs, tm, collectionReader): capture_stdout = cStringIO.StringIO() + collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt") exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "tests/wf/submit_keepref_wf.cwl"], @@ -709,7 +850,7 @@ class TestSubmit(unittest.TestCase): self.assertEqual(exited, 0) expect_container = { - 'priority': 1, + 'priority': 500, 'mounts': { '/var/spool/cwl': { 'writable': True, @@ -730,12 +871,13 @@ class TestSubmit(unittest.TestCase): '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', '--on-error=continue', + 'container_image': '999999999999999999999999999999d3+99', + 'command': ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'], 'cwd': '/var/spool/cwl', 'runtime_constraints': { @@ -744,7 +886,8 @@ class TestSubmit(unittest.TestCase): 'ram': 1073741824 }, 'use_existing': True, - 'properties': {} + 'properties': {}, + 'secret_mounts': {} } stubs.api.container_requests().create.assert_called_with( @@ -792,7 +935,7 @@ class TestSubmit(unittest.TestCase): self.assertEqual(exited, 0) expect_container = { - 'priority': 1, + 'priority': 500, 'mounts': { '/var/spool/cwl': { 'writable': True, @@ -829,7 +972,11 @@ class TestSubmit(unittest.TestCase): 'id': '#submit_tool.cwl/x'} ], 'requirements': [ - {'dockerPull': 'debian:8', 'class': 'DockerRequirement'} + { + 'dockerPull': 'debian:8', + 'class': 'DockerRequirement', + "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" + } ], 'id': '#submit_tool.cwl', 'outputs': [], @@ -846,12 +993,13 @@ class TestSubmit(unittest.TestCase): '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', '--on-error=continue', + 'container_image': "999999999999999999999999999999d3+99", + 'command': ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + '--eval-timeout=20', '--thread-count=4', + '--enable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], 'cwd': '/var/spool/cwl', 'runtime_constraints': { @@ -862,7 +1010,8 @@ class TestSubmit(unittest.TestCase): 'use_existing': True, 'properties': { "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37" - } + }, + 'secret_mounts': {} } stubs.api.container_requests().create.assert_called_with( @@ -907,8 +1056,62 @@ class TestSubmit(unittest.TestCase): expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["owner_uuid"] = project_uuid - expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', - '--enable-reuse', '--on-error=continue', '--project-uuid='+project_uuid, + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', + "--eval-timeout=20", "--thread-count=4", + '--enable-reuse', '--debug', '--on-error=continue', + '--project-uuid='+project_uuid, + '/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_eval_timeout(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60", + "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', '--disable-validate', + '--eval-timeout=60.0', '--thread-count=4', + '--enable-reuse', '--debug', '--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_thread_count(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20", + "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', '--disable-validate', + '--eval-timeout=20', '--thread-count=20', + '--enable-reuse', '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] stubs.api.container_requests().create.assert_called_with( @@ -929,7 +1132,7 @@ class TestSubmit(unittest.TestCase): except: logging.exception("") - stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "arvados/jobs:123" + stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "999999999999999999999999999999d5+99" expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) stubs.api.pipeline_instances().create.assert_called_with( @@ -949,19 +1152,79 @@ class TestSubmit(unittest.TestCase): except: logging.exception("") - stubs.expect_container_spec["container_image"] = "arvados/jobs:123" + stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99" + + 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_priority(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669", + "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["priority"] = 669 + + 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_wf_runner_resources(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", + "tests/wf/submit_wf_runner_resources.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["runtime_constraints"] = { + "API": True, + "vcpus": 2, + "ram": 2000 * 2**20 + } + expect_container["name"] = "submit_wf_runner_resources.cwl" + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [ + { + "class": "http://arvados.org/cwl#WorkflowRunnerResources", + "coresMin": 2, + "ramMin": 2000 + } + ] + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = { + "arv": "http://arvados.org/cwl#", + } + stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') + def tearDown(self): + arvados_cwl.arvdocker.arv_docker_clear_cache() @mock.patch("arvados.commands.keepdocker.find_one_image_hash") - @mock.patch("cwltool.docker.get_image") + @mock.patch("cwltool.docker.DockerCommandLineJob.get_image") @mock.patch("arvados.api") def test_arvados_jobs_image(self, api, get_image, find_one_image_hash): + arvados_cwl.arvdocker.arv_docker_clear_cache() + arvrunner = mock.MagicMock() arvrunner.project_uuid = "" api.return_value = mock.MagicMock() @@ -987,9 +1250,237 @@ class TestSubmit(unittest.TestCase): "properties": "" }], "items_available": 1, "offset": 0},) arvrunner.api.collections().create().execute.return_value = {"uuid": ""} - self.assertEqual("arvados/jobs:"+arvados_cwl.__version__, + arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb", + "portable_data_hash": "9999999999999999999999999999999b+99"} + self.assertEqual("9999999999999999999999999999999b+99", arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__)) + + @stubs + def test_submit_secrets(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", + "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"], + capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 0) + except: + logging.exception("") + + + expect_container = { + "command": [ + "arvados-cwl-runner", + "--local", + "--api=containers", + "--no-log-timestamps", + "--disable-validate", + "--eval-timeout=20", + '--thread-count=4', + "--enable-reuse", + '--debug', + "--on-error=continue", + "/var/lib/cwl/workflow.json#main", + "/var/lib/cwl/cwl.input.json" + ], + "container_image": "999999999999999999999999999999d3+99", + "cwd": "/var/spool/cwl", + "mounts": { + "/var/lib/cwl/cwl.input.json": { + "content": { + "pw": { + "$include": "/secrets/s0" + } + }, + "kind": "json" + }, + "/var/lib/cwl/workflow.json": { + "content": { + "$graph": [ + { + "$namespaces": { + "cwltool": "http://commonwl.org/cwltool#" + }, + "arguments": [ + "md5sum", + "example.conf" + ], + "class": "CommandLineTool", + "hints": [ + { + "class": "http://commonwl.org/cwltool#Secrets", + "secrets": [ + "#secret_job.cwl/pw" + ] + } + ], + "id": "#secret_job.cwl", + "inputs": [ + { + "id": "#secret_job.cwl/pw", + "type": "string" + } + ], + "outputs": [ + { + "id": "#secret_job.cwl/out", + "type": "stdout" + } + ], + "stdout": "hashed_example.txt", + "requirements": [ + { + "class": "InitialWorkDirRequirement", + "listing": [ + { + "entry": "username: user\npassword: $(inputs.pw)\n", + "entryname": "example.conf" + } + ] + } + ] + }, + { + "class": "Workflow", + "hints": [ + { + "class": "DockerRequirement", + "dockerPull": "debian:8", + "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" + }, + { + "class": "http://commonwl.org/cwltool#Secrets", + "secrets": [ + "#main/pw" + ] + } + ], + "id": "#main", + "inputs": [ + { + "id": "#main/pw", + "type": "string" + } + ], + "outputs": [ + { + "id": "#main/out", + "outputSource": "#main/step1/out", + "type": "File" + } + ], + "steps": [ + { + "id": "#main/step1", + "in": [ + { + "id": "#main/step1/pw", + "source": "#main/pw" + } + ], + "out": [ + "#main/step1/out" + ], + "run": "#secret_job.cwl" + } + ] + } + ], + "cwlVersion": "v1.0" + }, + "kind": "json" + }, + "/var/spool/cwl": { + "kind": "collection", + "writable": True + }, + "stdout": { + "kind": "file", + "path": "/var/spool/cwl/cwl.output.json" + } + }, + "name": "secret_wf.cwl", + "output_path": "/var/spool/cwl", + "priority": 500, + "properties": {}, + "runtime_constraints": { + "API": True, + "ram": 1073741824, + "vcpus": 1 + }, + "secret_mounts": { + "/secrets/s0": { + "content": "blorp", + "kind": "text" + } + }, + "state": "Committed", + "use_existing": True + } + + 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_request_uuid(self, stubs): + stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy" + + stubs.api.container_requests().update().execute.return_value = { + "uuid": stubs.expect_container_request_uuid, + "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz", + "state": "Queued" + } + + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy", + "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.container_requests().update.assert_called_with( + uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec), cluster_id="zzzzz") + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + @stubs + def test_submit_container_cluster_id(self, stubs): + capture_stdout = cStringIO.StringIO() + stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123" + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb", + "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) + + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(expect_container), cluster_id="zbbbb") + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + + @stubs + def test_submit_validate_cluster_id(self, stubs): + capture_stdout = cStringIO.StringIO() + stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123" + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zcccc", + "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, 1) + + class TestCreateTemplate(unittest.TestCase): existing_template_uuid = "zzzzz-d1hrv-validworkfloyml" @@ -1287,12 +1778,12 @@ class TestTemplateInputs(unittest.TestCase): "components": { "inputs_test.cwl": { 'runtime_constraints': { - 'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024 }, 'script_parameters': { 'cwl:tool': - '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main', + 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main', 'optionalFloatInput': None, 'fileInput': { 'type': 'File', @@ -1353,7 +1844,7 @@ class TestTemplateInputs(unittest.TestCase): params = expect_template[ "components"]["inputs_test.cwl"]["script_parameters"] params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt' - params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main' + params["cwl:tool"] = 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main' params["floatInput"]["value"] = 1.234 params["boolInput"]["value"] = True