X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/95e5ccacf6c1193b313fa90a6d39baafa2ba67d8..8352a6863cdcc2794108a71fd5b64e7b75f9dd20:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 8875b7d954..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': { @@ -137,7 +171,7 @@ def stubs(func): }], 'class': 'Directory' }, - 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main' + 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main' }, 'repository': 'arvados', 'script_version': 'master', @@ -151,7 +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": { @@ -169,7 +203,7 @@ def stubs(func): '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' @@ -243,7 +277,7 @@ def stubs(func): '--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': { @@ -273,10 +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", @@ -299,13 +340,14 @@ class TestSubmit(unittest.TestCase): }), 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) ]) @@ -642,7 +684,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("arvados_cwl.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") - @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None)) + @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): @@ -663,7 +705,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("arvados_cwl.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") - @mock.patch("arvados_cwl.ArvCwlRunner.make_output_collection", return_value = (None, None)) + @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): @@ -831,7 +873,7 @@ class TestSubmit(unittest.TestCase): }, 'state': 'Committed', 'output_path': '/var/spool/cwl', 'name': 'expect_arvworkflow.cwl#main', - 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'container_image': '999999999999999999999999999999d3+99', 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--eval-timeout=20', '--thread-count=4', @@ -930,7 +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': [], @@ -949,7 +995,7 @@ class TestSubmit(unittest.TestCase): }, 'state': 'Committed', 'output_path': '/var/spool/cwl', 'name': 'a test workflow', - 'container_image': 'arvados/jobs:'+arvados_cwl.__version__, + 'container_image': "999999999999999999999999999999d3+99", 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--no-log-timestamps', '--disable-validate', '--eval-timeout=20', '--thread-count=4', @@ -1086,7 +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( @@ -1106,7 +1152,7 @@ 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( @@ -1170,11 +1216,15 @@ class TestSubmit(unittest.TestCase): 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.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() @@ -1200,9 +1250,12 @@ 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() @@ -1231,7 +1284,7 @@ class TestSubmit(unittest.TestCase): "/var/lib/cwl/workflow.json#main", "/var/lib/cwl/cwl.input.json" ], - "container_image": "arvados/jobs:"+arvados_cwl.__version__, + "container_image": "999999999999999999999999999999d3+99", "cwd": "/var/spool/cwl", "mounts": { "/var/lib/cwl/cwl.input.json": { @@ -1293,7 +1346,8 @@ class TestSubmit(unittest.TestCase): "hints": [ { "class": "DockerRequirement", - "dockerPull": "debian:8" + "dockerPull": "debian:8", + "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" }, { "class": "http://commonwl.org/cwltool#Secrets", @@ -1391,11 +1445,42 @@ class TestSubmit(unittest.TestCase): logging.exception("") stubs.api.container_requests().update.assert_called_with( - uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec)) + 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" @@ -1693,12 +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', @@ -1759,7 +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