X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/4aee7d57faff02fc6b7b6f750dc22a29e58bb963..c340eecc7a03dd066792e5f046f087b8b3dfced6:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index d2c4d9c2ea..1b646a8e44 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -17,6 +17,8 @@ import logging import mock import sys import unittest +import cwltool.process +import re from io import BytesIO @@ -66,7 +68,7 @@ def stubs(func): stubs.keep_client = keep_client2 stubs.docker_images = { "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", "")], - "debian:8": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")], + "debian:buster-slim": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")], "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", "")], "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", "")], } @@ -93,6 +95,11 @@ def stubs(func): stubs.api.containers().current().execute.return_value = { "uuid": stubs.fake_container_uuid, } + stubs.api.config()["StorageClasses"].items.return_value = { + "default": { + "Default": True + } + }.items() class CollectionExecute(object): def __init__(self, exe): @@ -300,8 +307,8 @@ def stubs(func): 'secret_mounts': {}, 'state': 'Committed', 'command': ['arvados-cwl-runner', '--local', '--api=containers', - '--no-log-timestamps', '--disable-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], 'name': 'submit_wf.cwl', @@ -313,7 +320,7 @@ def stubs(func): 'vcpus': 1, 'ram': (1024+256)*1024*1024 }, - 'use_existing': True, + 'use_existing': False, 'properties': {}, 'secret_mounts': {} } @@ -335,116 +342,11 @@ def stubs(func): class TestSubmit(unittest.TestCase): - @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 - - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=jobs", "--debug", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - stubs.capture_stdout, sys.stderr, api_client=stubs.api) - - stubs.api.collections().create.assert_has_calls([ - mock.call(body=JsonDiffMatcher({ - 'manifest_text': - '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', - 'replication_desired': None, - 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', - }), ensure_unique_name=False), - mock.call(body=JsonDiffMatcher({ - 'manifest_text': - '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', - 'replication_desired': None, - 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)', - }), ensure_unique_name=False), - mock.call(body=JsonDiffMatcher({ - 'manifest_text': - ". 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) - ]) - - expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) - stubs.api.pipeline_instances().create.assert_called_with( - body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(stubs.capture_stdout.getvalue(), - stubs.expect_pipeline_uuid + '\n') - self.assertEqual(exited, 0) - - @mock.patch("time.sleep") - @stubs - def test_submit_no_reuse(self, stubs, tm): - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - stubs.capture_stdout, sys.stderr, api_client=stubs.api) - - expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) - expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False} - expect_pipeline["properties"] = {"run_options": {"enable_job_reuse": False}} - - stubs.api.pipeline_instances().create.assert_called_with( - body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(stubs.capture_stdout.getvalue(), - stubs.expect_pipeline_uuid + '\n') - self.assertEqual(exited, 0) - @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): - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - stubs.capture_stdout, sys.stderr, api_client=stubs.api) - - 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=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(stubs.capture_stdout.getvalue(), - stubs.expect_pipeline_uuid + '\n') - self.assertEqual(exited, 0) - - @mock.patch("time.sleep") - @stubs - def test_submit_runner_ram(self, stubs, tm): - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048", - "--api=jobs", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - stubs.capture_stdout, sys.stderr, api_client=stubs.api) - - expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) - expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048 + def setUp(self): + cwltool.process._names = set() + arvados_cwl.arvdocker.arv_docker_clear_cache() - stubs.api.pipeline_instances().create.assert_called_with( - body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(stubs.capture_stdout.getvalue(), - stubs.expect_pipeline_uuid + '\n') - self.assertEqual(exited, 0) @mock.patch("time.sleep") @stubs @@ -455,81 +357,6 @@ class TestSubmit(unittest.TestCase): stubs.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" - - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--debug", "--output-name", output_name, - "--api=jobs", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - stubs.capture_stdout, sys.stderr, api_client=stubs.api) - - 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(stubs.capture_stdout.getvalue(), - stubs.expect_pipeline_uuid + '\n') - self.assertEqual(exited, 0) - - @mock.patch("time.sleep") - @stubs - def test_submit_pipeline_name(self, stubs, tm): - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--debug", "--name=hello job 123", - "--api=jobs", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - stubs.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=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(stubs.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" - - exited = arvados_cwl.main( - ["--submit", "--no-wait", "--debug", "--output-tags", output_tags, - "--api=jobs", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - stubs.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:output_tags"] = output_tags - - stubs.api.pipeline_instances().create.assert_called_with( - body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(stubs.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( - ["--submit", "--no-wait", "--debug", - "--project-uuid", project_uuid, - "--api=jobs", - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - sys.stdout, sys.stderr, api_client=stubs.api) - self.assertEqual(exited, 0) - - 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): @@ -560,6 +387,19 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) + + @stubs + def test_submit_container_tool(self, stubs): + # test for issue #16139 + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", + "tests/tool/tool_with_sf.cwl", "tests/tool/tool_with_sf.yml"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + + self.assertEqual(stubs.capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + self.assertEqual(exited, 0) + @stubs def test_submit_container_no_reuse(self, stubs): exited = arvados_cwl.main( @@ -570,8 +410,8 @@ 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-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -594,8 +434,8 @@ 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-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] expect_container["use_existing"] = False @@ -626,8 +466,8 @@ 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-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=stop', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -649,8 +489,8 @@ 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-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", "--output-name="+output_name, '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -671,8 +511,8 @@ 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-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", "--debug", "--storage-classes=foo", '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -683,11 +523,35 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @mock.patch("arvados_cwl.task_queue.TaskQueue") + @stubs + def test_submit_multiple_storage_classes(self, stubs): + exited = arvados_cwl.main( + ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + + expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', + '--enable-reuse', "--collection-cache-size=256", "--debug", + "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--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(stubs.capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + self.assertEqual(exited, 0) + + @mock.patch("cwltool.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") - @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None)) + @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection") @stubs def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq): + final_output_c = arvados.collection.Collection() + make_output.return_value = ({},final_output_c) + def set_final_output(job_order, output_callback, runtimeContext): output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") return [] @@ -696,16 +560,19 @@ class TestSubmit(unittest.TestCase): 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) + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') self.assertEqual(exited, 0) - @mock.patch("arvados_cwl.task_queue.TaskQueue") + @mock.patch("cwltool.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") - @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None)) + @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection") @stubs def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq): + final_output_c = arvados.collection.Collection() + make_output.return_value = ({},final_output_c) + def set_final_output(job_order, output_callback, runtimeContext): output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") return [] @@ -714,11 +581,32 @@ class TestSubmit(unittest.TestCase): 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) + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') self.assertEqual(exited, 0) + @mock.patch("cwltool.task_queue.TaskQueue") + @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") + @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection") + @stubs + def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq): + final_output_c = arvados.collection.Collection() + make_output.return_value = ({},final_output_c) + + def set_final_output(job_order, output_callback, runtimeContext): + output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") + return [] + job.side_effect = set_final_output + + exited = arvados_cwl.main( + ["--debug", "--local", + "tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + + make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') + self.assertEqual(exited, 0) + @stubs def test_submit_container_output_ttl(self, stubs): exited = arvados_cwl.main( @@ -728,8 +616,8 @@ 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-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', "--intermediate-output-ttl=3600", @@ -751,8 +639,8 @@ 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-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', "--trash-intermediate", @@ -775,8 +663,8 @@ 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-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", "--output-tags="+output_tags, '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -807,6 +695,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("time.sleep") @stubs def test_submit_file_keepref(self, stubs, tm, collectionReader): + collectionReader().exists.return_value = True collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt") exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -852,8 +741,8 @@ class TestSubmit(unittest.TestCase): 'name': 'expect_arvworkflow.cwl#main', 'container_image': '999999999999999999999999999999d3+99', 'command': ['arvados-cwl-runner', '--local', '--api=containers', - '--no-log-timestamps', '--disable-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'], 'cwd': '/var/spool/cwl', @@ -862,7 +751,7 @@ class TestSubmit(unittest.TestCase): 'vcpus': 1, 'ram': 1342177280 }, - 'use_existing': True, + 'use_existing': False, 'properties': {}, 'secret_mounts': {} } @@ -873,28 +762,6 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @mock.patch("arvados.collection.CollectionReader") - @mock.patch("time.sleep") - @stubs - def test_submit_jobs_keepref(self, stubs, tm, reader): - 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"], - stubs.capture_stdout, sys.stderr, api_client=stubs.api) - - 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)) - self.assertEqual(exited, 0) - @mock.patch("time.sleep") @stubs def test_submit_arvworkflow(self, stubs, tm): @@ -945,7 +812,7 @@ class TestSubmit(unittest.TestCase): ], 'requirements': [ { - 'dockerPull': 'debian:8', + 'dockerPull': 'debian:buster-slim', 'class': 'DockerRequirement', "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" } @@ -969,8 +836,8 @@ class TestSubmit(unittest.TestCase): 'name': 'a test workflow', 'container_image': "999999999999999999999999999999d3+99", 'command': ['arvados-cwl-runner', '--local', '--api=containers', - '--no-log-timestamps', '--disable-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], 'cwd': '/var/spool/cwl', @@ -979,7 +846,7 @@ class TestSubmit(unittest.TestCase): 'vcpus': 1, 'ram': 1342177280 }, - 'use_existing': True, + 'use_existing': False, 'properties': { "template_uuid": "962eh-7fd4e-gkbzl62qqtfig37" }, @@ -1025,6 +892,7 @@ class TestSubmit(unittest.TestCase): @stubs def test_submit_container_project(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + stubs.api.groups().get().execute.return_value = {"group_class": "project"} exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid, "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], @@ -1033,8 +901,8 @@ 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', '--disable-validate', - "--eval-timeout=20", "--thread-count=1", + '--no-log-timestamps', '--disable-validate', '--disable-color', + "--eval-timeout=20", "--thread-count=0", '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', '--project-uuid='+project_uuid, @@ -1055,8 +923,8 @@ 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-validate', - '--eval-timeout=60.0', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=60.0', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -1076,8 +944,8 @@ 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-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=500", '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -1098,7 +966,7 @@ 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-validate', + '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=20', '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', @@ -1110,22 +978,6 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs - def test_submit_job_runner_image(self, stubs): - 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"], - stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) - - 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( - body=JsonDiffMatcher(expect_pipeline)) - self.assertEqual(stubs.capture_stdout.getvalue(), - stubs.expect_pipeline_uuid + '\n') - self.assertEqual(exited, 0) - @stubs def test_submit_container_runner_image(self, stubs): exited = arvados_cwl.main( @@ -1184,8 +1036,8 @@ class TestSubmit(unittest.TestCase): "arv": "http://arvados.org/cwl#", } expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers', - '--no-log-timestamps', '--disable-validate', - '--eval-timeout=20', '--thread-count=1', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=512", '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -1249,8 +1101,9 @@ class TestSubmit(unittest.TestCase): "--api=containers", "--no-log-timestamps", "--disable-validate", + "--disable-color", "--eval-timeout=20", - '--thread-count=1', + '--thread-count=0', "--enable-reuse", "--collection-cache-size=256", '--debug', @@ -1299,7 +1152,10 @@ class TestSubmit(unittest.TestCase): "outputs": [ { "id": "#secret_job.cwl/out", - "type": "stdout" + "type": "File", + "outputBinding": { + "glob": "hashed_example.txt" + } } ], "stdout": "hashed_example.txt", @@ -1320,7 +1176,7 @@ class TestSubmit(unittest.TestCase): "hints": [ { "class": "DockerRequirement", - "dockerPull": "debian:8", + "dockerPull": "debian:buster-slim", "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" }, { @@ -1390,7 +1246,7 @@ class TestSubmit(unittest.TestCase): } }, "state": "Committed", - "use_existing": True + "use_existing": False } stubs.api.container_requests().create.assert_called_with( @@ -1447,9 +1303,35 @@ class TestSubmit(unittest.TestCase): stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 1) + @stubs + def test_submit_validate_project_uuid(self, stubs): + # Fails with bad cluster prefix + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzb-j7d0g-zzzzzzzzzzzzzzz", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 1) + + # Project lookup fails + stubs.api.groups().get().execute.side_effect = Exception("Bad project") + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-j7d0g-zzzzzzzzzzzzzzx", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 1) + + # It should work this time because it is looking up a user (and only group is stubbed out to fail) + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-tpzed-zzzzzzzzzzzzzzx", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + self.assertEqual(exited, 0) + + @mock.patch("arvados.collection.CollectionReader") @stubs def test_submit_uuid_inputs(self, stubs, collectionReader): + collectionReader().exists.return_value = True collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt") def list_side_effect(**kwargs): m = mock.MagicMock() @@ -1508,8 +1390,8 @@ class TestSubmit(unittest.TestCase): stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 1) - self.assertRegexpMatches( - capture_stderr.getvalue(), + self.assertRegex( + re.sub(r'[ \n]+', ' ', capture_stderr.getvalue()), r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99") finally: cwltool_logger.removeHandler(stderr_logger) @@ -1531,138 +1413,26 @@ class TestSubmit(unittest.TestCase): try: self.assertEqual(exited, 1) - self.assertRegexpMatches( + self.assertRegex( capture_stderr.getvalue(), r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found") finally: cwltool_logger.removeHandler(stderr_logger) -class TestCreateTemplate(unittest.TestCase): - existing_template_uuid = "zzzzz-p5p6p-validworkfloyml" - - def _adjust_script_params(self, expect_component): - expect_component['script_parameters']['x'] = { - 'dataclass': 'File', - 'required': True, - 'type': 'File', - 'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', - } - expect_component['script_parameters']['y'] = { - 'dataclass': 'Collection', - 'required': True, - 'type': 'Directory', - 'value': '99999999999999999999999999999998+99', - } - expect_component['script_parameters']['z'] = { - 'dataclass': 'Collection', - 'required': True, - 'type': 'Directory', - } - - @stubs - def test_create(self, stubs): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - - exited = arvados_cwl.main( - ["--create-workflow", "--debug", - "--api=jobs", - "--project-uuid", project_uuid, - "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], - stubs.capture_stdout, sys.stderr, api_client=stubs.api) - - 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, - }, - "name": "submit_wf.cwl", - "owner_uuid": project_uuid, - } - stubs.api.pipeline_templates().create.assert_called_with( - body=JsonDiffMatcher(expect_template), ensure_unique_name=True) - - self.assertEqual(stubs.capture_stdout.getvalue(), - stubs.expect_pipeline_template_uuid + '\n') - self.assertEqual(exited, 0) - - @stubs - def test_create_name(self, stubs): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - - 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"], - stubs.capture_stdout, sys.stderr, api_client=stubs.api) - - 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(stubs.capture_stdout.getvalue(), - stubs.expect_pipeline_template_uuid + '\n') - self.assertEqual(exited, 0) - - @stubs - def test_update_name(self, stubs): - project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' - - 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"], - stubs.capture_stdout, sys.stderr, api_client=stubs.api) - - 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(stubs.capture_stdout.getvalue(), - self.existing_template_uuid + '\n') - self.assertEqual(exited, 0) - - class TestCreateWorkflow(unittest.TestCase): existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml" expect_workflow = StripYAMLComments( - open("tests/wf/expect_packed.cwl").read()) + open("tests/wf/expect_upload_packed.cwl").read().rstrip()) + + def setUp(self): + cwltool.process._names = set() + arvados_cwl.arvdocker.arv_docker_clear_cache() @stubs def test_create(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + stubs.api.groups().get().execute.return_value = {"group_class": "project"} exited = arvados_cwl.main( ["--create-workflow", "--debug", @@ -1692,6 +1462,7 @@ class TestCreateWorkflow(unittest.TestCase): @stubs def test_create_name(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + stubs.api.groups().get().execute.return_value = {"group_class": "project"} exited = arvados_cwl.main( ["--create-workflow", "--debug", @@ -1719,26 +1490,6 @@ class TestCreateWorkflow(unittest.TestCase): stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) - @stubs - def test_incompatible_api(self, stubs): - capture_stderr = StringIO() - acr_logger = logging.getLogger('arvados.cwl-runner') - stderr_logger = logging.StreamHandler(capture_stderr) - acr_logger.addHandler(stderr_logger) - - try: - 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)) - finally: - acr_logger.removeHandler(stderr_logger) @stubs def test_update(self, stubs): @@ -1787,6 +1538,7 @@ class TestCreateWorkflow(unittest.TestCase): @stubs def test_create_collection_per_tool(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + stubs.api.groups().get().execute.return_value = {"group_class": "project"} exited = arvados_cwl.main( ["--create-workflow", "--debug", @@ -1796,7 +1548,7 @@ class TestCreateWorkflow(unittest.TestCase): stubs.capture_stdout, sys.stderr, api_client=stubs.api) toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl" - expect_workflow = StripYAMLComments(open(toolfile).read()) + expect_workflow = StripYAMLComments(open(toolfile).read().rstrip()) body = { "workflow": { @@ -1813,81 +1565,40 @@ class TestCreateWorkflow(unittest.TestCase): stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) -class TestTemplateInputs(unittest.TestCase): - expect_template = { - "components": { - "inputs_test.cwl": { - 'runtime_constraints': { - 'docker_image': '999999999999999999999999999999d3+99', - 'min_ram_mb_per_node': 1024 - }, - 'script_parameters': { - 'cwl:tool': - 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main', - 'optionalFloatInput': None, - 'fileInput': { - 'type': 'File', - 'dataclass': 'File', - 'required': True, - 'title': "It's a file; we expect to find some characters in it.", - 'description': 'If there were anything further to say, it would be said here,\nor here.' - }, - 'floatInput': { - 'type': 'float', - 'dataclass': 'number', - 'required': True, - 'title': 'Floats like a duck', - 'default': 0.1, - 'value': 0.1, - }, - 'optionalFloatInput': { - 'type': ['null', 'float'], - 'dataclass': 'number', - 'required': False, - }, - 'boolInput': { - 'type': 'boolean', - 'dataclass': 'boolean', - 'required': True, - 'title': 'True or false?', - }, - }, - 'repository': 'arvados', - 'script_version': 'master', - 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', - 'script': 'cwl-runner', - }, - }, - "name": "inputs_test.cwl", - } - @stubs - def test_inputs_empty(self, stubs): + def test_create_with_imports(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + stubs.api.groups().get().execute.return_value = {"group_class": "project"} + exited = arvados_cwl.main( - ["--debug", "--api=jobs", "--create-template", - "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"], + ["--create-workflow", "--debug", + "--api=containers", + "--project-uuid", project_uuid, + "tests/wf/feddemo/feddemo.cwl"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) - stubs.api.pipeline_templates().create.assert_called_with( - body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True) + stubs.api.pipeline_templates().create.refute_called() + stubs.api.container_requests().create.refute_called() + self.assertEqual(stubs.capture_stdout.getvalue(), + stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) @stubs - def test_inputs(self, stubs): + def test_create_with_no_input(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + stubs.api.groups().get().execute.return_value = {"group_class": "project"} + exited = arvados_cwl.main( - ["--api=jobs", "--create-template", - "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"], + ["--create-workflow", "--debug", + "--api=containers", + "--project-uuid", project_uuid, + "tests/wf/revsort/revsort.cwl"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) - expect_template = copy.deepcopy(self.expect_template) - params = expect_template[ - "components"]["inputs_test.cwl"]["script_parameters"] - params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt' - params["cwl:tool"] = 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main' - params["floatInput"]["value"] = 1.234 - params["boolInput"]["value"] = True + stubs.api.pipeline_templates().create.refute_called() + stubs.api.container_requests().create.refute_called() - stubs.api.pipeline_templates().create.assert_called_with( - body=JsonDiffMatcher(expect_template), ensure_unique_name=True) + self.assertEqual(stubs.capture_stdout.getvalue(), + stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0)