X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/0d62edcb9d25bf4dcdb20d8872ea7b438e12fc59..6164f448f5828e1f4649fae4fe7866b8f082614c:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 4418ee3fd1..3d6b91536a 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -1,3 +1,7 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + import copy import cStringIO import functools @@ -14,9 +18,11 @@ import arvados_cwl import arvados_cwl.runner import arvados.keep -from .matcher import JsonDiffMatcher +from .matcher import JsonDiffMatcher, StripYAMLComments from .mock_discovery import get_rootDesc +import ruamel.yaml as yaml + _rootDesc = None def stubs(func): @@ -32,7 +38,6 @@ def stubs(func): stubs.events = events stubs.keepdocker = keepdocker - def putstub(p, **kwargs): return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p)) keep_client1().put.side_effect = putstub @@ -51,33 +56,37 @@ def stubs(func): "uuid": stubs.fake_user_uuid, } stubs.api.collections().list().execute.return_value = {"items": []} - stubs.api.collections().create().execute.side_effect = ({ - "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz1", - "portable_data_hash": "99999999999999999999999999999991+99", - "manifest_text": "" - }, { - "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2", - "portable_data_hash": "99999999999999999999999999999992+99", - "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt" - }, - { - "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz4", - "portable_data_hash": "99999999999999999999999999999994+99", - "manifest_text": "" - }, - { - "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz5", - "portable_data_hash": "99999999999999999999999999999995+99", - "manifest_text": "" - }, - { - "uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz6", - "portable_data_hash": "99999999999999999999999999999996+99", - "manifest_text": "" - } - ) - stubs.api.collections().get().execute.return_value = { - "portable_data_hash": "99999999999999999999999999999993+99", "manifest_text": "./tool 00000000000000000000000000000000+0 0:0:submit_tool.cwl 0:0:blub.txt"} + + class CollectionExecute(object): + def __init__(self, exe): + self.exe = exe + def execute(self, num_retries=None): + return self.exe + + def collection_createstub(created_collections, body, ensure_unique_name=None): + mt = body["manifest_text"] + uuid = "zzzzz-4zz18-zzzzzzzzzzzzzz%d" % len(created_collections) + pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt)) + created_collections[uuid] = { + "uuid": uuid, + "portable_data_hash": pdh, + "manifest_text": mt + } + return CollectionExecute(created_collections[uuid]) + + def collection_getstub(created_collections, uuid): + for v in created_collections.itervalues(): + if uuid in (v["uuid"], v["portable_data_hash"]): + return CollectionExecute(v) + + created_collections = { + "99999999999999999999999999999998+99": { + "uuid": "", + "portable_data_hash": "99999999999999999999999999999998+99", + "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt" + }} + stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections) + stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections) stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz" stubs.api.jobs().create().execute.return_value = { @@ -104,7 +113,7 @@ def stubs(func): 'script_parameters': { 'x': { 'basename': 'blorp.txt', - 'location': 'keep:99999999999999999999999999999994+99/blorp.txt', + 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', 'class': 'File' }, 'y': { @@ -121,11 +130,11 @@ def stubs(func): }], 'class': 'Directory' }, - 'cwl:tool': - '99999999999999999999999999999991+99/wf/submit_wf.cwl' + 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/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 +147,30 @@ 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:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', + "nameext": ".txt", + "nameroot": "blorp" + }}, 'z': {"value": {'basename': 'anonymous', 'class': 'Directory', 'listing': [ - {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'} + { + 'basename': 'renamed.txt', + 'class': 'File', 'location': + 'keep:99999999999999999999999999999998+99/file1.txt', + "nameext": ".txt", + "nameroot": "renamed" + } ]}}, - 'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl', - 'arv:enable_reuse': True + 'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/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 +187,9 @@ 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': { @@ -171,9 +197,9 @@ 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', @@ -182,10 +208,24 @@ def stubs(func): '/var/lib/cwl/cwl.input.json': { 'kind': 'json', 'content': { - 'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}, - 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:99999999999999999999999999999994+99/blorp.txt'}, + 'y': { + 'basename': '99999999999999999999999999999998+99', + 'location': 'keep:99999999999999999999999999999998+99', + 'class': 'Directory'}, + 'x': { + 'basename': u'blorp.txt', + 'class': 'File', + 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', + "nameext": ".txt", + "nameroot": "blorp" + }, 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [ - {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'} + {'basename': 'renamed.txt', + 'class': 'File', + 'location': 'keep:99999999999999999999999999999998+99/file1.txt', + "nameext": ".txt", + "nameroot": "renamed" + } ]} }, 'kind': 'json' @@ -193,7 +233,9 @@ def stubs(func): }, 'state': 'Committed', 'owner_uuid': None, - 'command': ['arvados-cwl-runner', '--local', '--api=containers', '--enable-reuse', '/var/lib/cwl/workflow/submit_wf.cwl', '/var/lib/cwl/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', @@ -223,44 +265,45 @@ 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), - mock.call().execute(num_retries=4), - mock.call(body={ + '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', + 'replication_desired': None, + 'name': 'submit_tool.cwl dependencies', + }), ensure_unique_name=True), + 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(body=JsonDiffMatcher({ + 'manifest_text': + '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217: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, {'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') @@ -270,14 +313,32 @@ 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=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), @@ -294,9 +355,9 @@ 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=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), @@ -325,9 +386,9 @@ 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(), @@ -344,11 +405,11 @@ class TestSubmit(unittest.TestCase): capture_stdout, sys.stderr, api_client=stubs.api) self.assertEqual(exited, 0) - stubs.expect_pipeline_instance["name"] = "hello job 123" - expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance) + 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') @@ -364,9 +425,9 @@ 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=JsonDiffMatcher(expect_pipeline)) self.assertEqual(capture_stdout.getvalue(), @@ -402,29 +463,18 @@ class TestSubmit(unittest.TestCase): logging.exception("") 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), - mock.call().execute(num_retries=4), - mock.call(body={ + '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n', + 'replication_desired': None, + 'name': 'submit_tool.cwl dependencies', + }), ensure_unique_name=True), + 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)]) expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( @@ -444,9 +494,34 @@ 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/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=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), @@ -466,9 +541,59 @@ 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/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=JsonDiffMatcher(expect_container)) + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + + + @stubs + def test_submit_container_output_ttl(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600", + "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=continue', + "--intermediate-output-ttl=3600", + '/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_trash_intermediate(self, stubs): + capture_stdout = cStringIO.StringIO() + try: + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate", + "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=continue', + "--trash-intermediate", + '/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(), @@ -488,9 +613,11 @@ 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/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=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), @@ -508,9 +635,9 @@ 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=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), @@ -569,7 +696,9 @@ class TestSubmit(unittest.TestCase): '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/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, @@ -584,6 +713,31 @@ class TestSubmit(unittest.TestCase): 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): @@ -611,9 +765,23 @@ 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': [ { @@ -628,19 +796,6 @@ 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': [] } ] } @@ -656,7 +811,9 @@ class TestSubmit(unittest.TestCase): 'output_path': '/var/spool/cwl', '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/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, @@ -686,11 +843,52 @@ class TestSubmit(unittest.TestCase): except: logging.exception("") - stubs.expect_container_spec["name"] = "hello container 123" + 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=expect_container) + body=JsonDiffMatcher(expect_container)) self.assertEqual(capture_stdout.getvalue(), stubs.expect_container_request_uuid + '\n') @@ -703,18 +901,8 @@ class TestSubmit(unittest.TestCase): arvrunner.project_uuid = "" api.return_value = mock.MagicMock() arvrunner.api = api.return_value - arvrunner.api.links().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0}, - {"items": [], "items_available": 0, "offset": 0}, - {"items": [], "items_available": 0, "offset": 0}, - {"items": [{"created_at": "", - "head_uuid": "", - "link_class": "docker_image_hash", - "name": "123456", - "owner_uuid": "", - "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}, - {"items": [], "items_available": 0, "offset": 0}, - {"items": [{"created_at": "", - "head_uuid": "", + arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "", + "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb", "link_class": "docker_image_repo+tag", "name": "arvados/jobs:"+arvados_cwl.__version__, "owner_uuid": "", @@ -724,19 +912,18 @@ class TestSubmit(unittest.TestCase): "link_class": "docker_image_hash", "name": "123456", "owner_uuid": "", - "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0} , + "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0} ) find_one_image_hash.return_value = "123456" - arvrunner.api.collections().list().execute.side_effect = ({"items": [], "items_available": 0, "offset": 0}, - {"items": [{"uuid": "", + arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb", "owner_uuid": "", "manifest_text": "", "properties": "" - }], "items_available": 1, "offset": 0}, - {"items": [{"uuid": ""}], "items_available": 1, "offset": 0}) + }], "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): existing_template_uuid = "zzzzz-d1hrv-validworkfloyml" @@ -746,7 +933,7 @@ class TestCreateTemplate(unittest.TestCase): 'dataclass': 'File', 'required': True, 'type': 'File', - 'value': '99999999999999999999999999999994+99/blorp.txt', + 'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', } expect_component['script_parameters']['y'] = { 'dataclass': 'Collection', @@ -865,7 +1052,8 @@ class TestCreateTemplate(unittest.TestCase): class TestCreateWorkflow(unittest.TestCase): existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml" - expect_workflow = open("tests/wf/expect_packed.cwl").read() + expect_workflow = StripYAMLComments( + open("tests/wf/expect_packed.cwl").read()) @stubs def test_create(self, stubs): @@ -998,6 +1186,37 @@ class TestCreateWorkflow(unittest.TestCase): self.existing_workflow_uuid + '\n') + @stubs + def test_create_collection_per_tool(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + + capture_stdout = cStringIO.StringIO() + + exited = arvados_cwl.main( + ["--create-workflow", "--debug", + "--api=containers", + "--project-uuid", project_uuid, + "tests/collection_per_tool/collection_per_tool.cwl"], + capture_stdout, sys.stderr, api_client=stubs.api) + self.assertEqual(exited, 0) + + toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl" + expect_workflow = StripYAMLComments(open(toolfile).read()) + + body = { + "workflow": { + "owner_uuid": project_uuid, + "name": "collection_per_tool.cwl", + "description": "", + "definition": expect_workflow, + } + } + stubs.api.workflows().create.assert_called_with( + body=JsonDiffMatcher(body)) + + self.assertEqual(capture_stdout.getvalue(), + stubs.expect_workflow_uuid + '\n') + class TestTemplateInputs(unittest.TestCase): expect_template = { "components": { @@ -1008,8 +1227,7 @@ class TestTemplateInputs(unittest.TestCase): }, 'script_parameters': { 'cwl:tool': - '99999999999999999999999999999991+99/' - 'wf/inputs_test.cwl', + '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main', 'optionalFloatInput': None, 'fileInput': { 'type': 'File', @@ -1039,7 +1257,8 @@ class TestTemplateInputs(unittest.TestCase): }, }, 'repository': 'arvados', - 'script_version': arvados_cwl.__version__, + 'script_version': 'master', + 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', 'script': 'cwl-runner', }, }, @@ -1068,7 +1287,8 @@ 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"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt' + params["cwl:tool"] = '6c5ee1cd606088106d9f28367cde1e41+60/workflow.cwl#main' params["floatInput"]["value"] = 1.234 params["boolInput"]["value"] = True