X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b9262c0e8c04f6b3d68f1ca301cc2ec56c2ef164..8c97b429803908fe13052dc788dfc313001c83b2:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index 61892bf2a4..604d66756e 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -19,6 +19,7 @@ import sys import unittest import cwltool.process import re +import os from io import BytesIO @@ -45,302 +46,338 @@ import ruamel.yaml as yaml _rootDesc = None -def stubs(func): - @functools.wraps(func) - @mock.patch("arvados.commands.keepdocker.list_images_in_arv") - @mock.patch("arvados.collection.KeepClient") - @mock.patch("arvados.keep.KeepClient") - @mock.patch("arvados.events.subscribe") - def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs): - class Stubs(object): - pass - stubs = Stubs() - 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 - keep_client1.put.side_effect = putstub - keep_client2().put.side_effect = putstub - keep_client2.put.side_effect = putstub - - stubs.keep_client = keep_client2 - stubs.docker_images = { - "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", {})], - "debian:buster-slim": [("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 +def stubs(wfdetails=('submit_wf.cwl', None)): + def outer_wrapper(func, *rest): + @functools.wraps(func) + @mock.patch("arvados_cwl.arvdocker.determine_image_id") + @mock.patch("uuid.uuid4") + @mock.patch("arvados.commands.keepdocker.list_images_in_arv") + @mock.patch("arvados.collection.KeepClient") + @mock.patch("arvados.keep.KeepClient") + @mock.patch("arvados.events.subscribe") + def wrapped(self, events, keep_client1, keep_client2, keepdocker, + uuid4, determine_image_id, *args, **kwargs): + class Stubs(object): + pass + + wfname = wfdetails[0] + wfpath = wfdetails[1] + + stubs = Stubs() + stubs.events = events + stubs.keepdocker = keepdocker + + uuid4.side_effect = ["df80736f-f14d-4b10-b2e3-03aa27f034bb", "df80736f-f14d-4b10-b2e3-03aa27f034b1", + "df80736f-f14d-4b10-b2e3-03aa27f034b2", "df80736f-f14d-4b10-b2e3-03aa27f034b3", + "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5"] + + determine_image_id.return_value = None + + def putstub(p, **kwargs): + return "%s+%i" % (hashlib.md5(p).hexdigest(), len(p)) + keep_client1().put.side_effect = putstub + keep_client1.put.side_effect = putstub + keep_client2().put.side_effect = putstub + keep_client2.put.side_effect = putstub + + stubs.keep_client = keep_client2 + stubs.docker_images = { + "arvados/jobs:"+arvados_cwl.__version__: [("zzzzz-4zz18-zzzzzzzzzzzzzd3", {})], + "debian:buster-slim": [("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, project_uuid=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.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz" + stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz" - if sys.version_info[0] < 3: - stubs.capture_stdout = BytesIO() - else: - stubs.capture_stdout = StringIO() + if sys.version_info[0] < 3: + stubs.capture_stdout = BytesIO() + else: + stubs.capture_stdout = StringIO() - stubs.api = mock.MagicMock() - stubs.api._rootDesc = get_rootDesc() - stubs.api._rootDesc["uuidPrefix"] = "zzzzz" - stubs.api._rootDesc["revision"] = "20210628" + stubs.api = mock.MagicMock() + stubs.api._rootDesc = get_rootDesc() + stubs.api._rootDesc["uuidPrefix"] = "zzzzz" + stubs.api._rootDesc["revision"] = "20210628" - stubs.api.users().current().execute.return_value = { - "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, - } - stubs.api.config()["StorageClasses"].items.return_value = { - "default": { - "Default": True + stubs.api.users().current().execute.return_value = { + "uuid": stubs.fake_user_uuid, } - }.items() - - 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"].encode('utf-8') - uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%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.decode('utf-8') - } - return CollectionExecute(created_collections[uuid]) - - def collection_getstub(created_collections, uuid): - for v in viewvalues(created_collections): - 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" - }, - "99999999999999999999999999999997+99": { - "uuid": "", - "portable_data_hash": "99999999999999999999999999999997+99", - "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt" - }, - "99999999999999999999999999999994+99": { - "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().list().execute.return_value = {"items": []} + stubs.api.containers().current().execute.return_value = { + "uuid": stubs.fake_container_uuid, } - } - 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 = { - "uuid": stubs.expect_job_uuid, - "state": "Queued", - } - - stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz" - stubs.api.container_requests().create().execute.return_value = { - "uuid": stubs.expect_container_request_uuid, - "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz", - "state": "Queued" - } - - stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz" - stubs.api.pipeline_templates().create().execute.return_value = { - "uuid": stubs.expect_pipeline_template_uuid, - } - stubs.expect_job_spec = { - 'runtime_constraints': { - 'docker_image': '999999999999999999999999999999d3+99', - 'min_ram_mb_per_node': 1024 - }, - 'script_parameters': { - 'x': { - 'basename': 'blorp.txt', - 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', - 'class': 'File' + stubs.api.config()["StorageClasses"].items.return_value = { + "default": { + "Default": True + } + }.items() + + 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"].encode('utf-8') + uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%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.decode('utf-8') + } + return CollectionExecute(created_collections[uuid]) + + def collection_getstub(created_collections, uuid): + for v in viewvalues(created_collections): + 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" }, - 'y': { - 'basename': '99999999999999999999999999999998+99', - 'location': 'keep:99999999999999999999999999999998+99', - 'class': 'Directory' + "99999999999999999999999999999997+99": { + "uuid": "", + "portable_data_hash": "99999999999999999999999999999997+99", + "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt" }, - 'z': { - 'basename': 'anonymous', - "listing": [{ - "basename": "renamed.txt", - "class": "File", - "location": "keep:99999999999999999999999999999998+99/file1.txt", - "size": 0 - }], - 'class': 'Directory' + "99999999999999999999999999999994+99": { + "uuid": "", + "portable_data_hash": "99999999999999999999999999999994+99", + "manifest_text": ". 99999999999999999999999999999994+99 0:0:expect_arvworkflow.cwl" }, - 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main' - }, - 'repository': 'arvados', - 'script_version': 'master', - 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', - 'script': 'cwl-runner' - } - stubs.pipeline_component = stubs.expect_job_spec.copy() - stubs.expect_pipeline_instance = { - 'name': 'submit_wf.cwl', - 'state': 'RunningOnServer', - 'owner_uuid': None, - "components": { - "cwl-runner": { - '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": { - 'basename': 'blorp.txt', - 'class': 'File', - 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', - "size": 16 - }}, - 'z': {"value": {'basename': 'anonymous', 'class': 'Directory', - 'listing': [ - { - 'basename': 'renamed.txt', - 'class': 'File', 'location': - 'keep:99999999999999999999999999999998+99/file1.txt', - 'size': 0 - } - ]}}, - 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main', - 'arv:debug': True, - 'arv:enable_reuse': True, - 'arv:on_error': 'continue' - }, - 'repository': 'arvados', - 'script_version': 'master', - 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', - 'script': 'cwl-runner', - 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'} + "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.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance) - stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz" - stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid - stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create) - stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = { - "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", - "state": "Queued" - } - stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create - stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job + 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 = { + "uuid": stubs.expect_job_uuid, + "state": "Queued", + } - with open("tests/wf/submit_wf_packed.cwl") as f: - expect_packed_workflow = yaml.round_trip_load(f) + stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz" + stubs.api.container_requests().create().execute.return_value = { + "uuid": stubs.expect_container_request_uuid, + "container_uuid": "zzzzz-dz642-zzzzzzzzzzzzzzz", + "state": "Queued" + } - stubs.expect_container_spec = { - 'priority': 500, - 'mounts': { - '/var/spool/cwl': { - 'writable': True, - 'kind': 'collection' - }, - '/var/lib/cwl/workflow.json': { - 'content': expect_packed_workflow, - 'kind': 'json' + stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz" + stubs.api.pipeline_templates().create().execute.return_value = { + "uuid": stubs.expect_pipeline_template_uuid, + } + stubs.expect_job_spec = { + 'runtime_constraints': { + 'docker_image': '999999999999999999999999999999d3+99', + 'min_ram_mb_per_node': 1024 }, - 'stdout': { - 'path': '/var/spool/cwl/cwl.output.json', - 'kind': 'file' + 'script_parameters': { + 'x': { + 'basename': 'blorp.txt', + 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', + 'class': 'File' + }, + 'y': { + 'basename': '99999999999999999999999999999998+99', + 'location': 'keep:99999999999999999999999999999998+99', + 'class': 'Directory' + }, + 'z': { + 'basename': 'anonymous', + "listing": [{ + "basename": "renamed.txt", + "class": "File", + "location": "keep:99999999999999999999999999999998+99/file1.txt", + "size": 0 + }], + 'class': 'Directory' + }, + 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main' }, - '/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:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', - "size": 16 + 'repository': 'arvados', + 'script_version': 'master', + 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', + 'script': 'cwl-runner' + } + stubs.pipeline_component = stubs.expect_job_spec.copy() + stubs.expect_pipeline_instance = { + 'name': 'submit_wf.cwl', + 'state': 'RunningOnServer', + 'owner_uuid': None, + "components": { + "cwl-runner": { + '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": { + 'basename': 'blorp.txt', + 'class': 'File', + 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', + "size": 16 + }}, + 'z': {"value": {'basename': 'anonymous', 'class': 'Directory', + 'listing': [ + { + 'basename': 'renamed.txt', + 'class': 'File', 'location': + 'keep:99999999999999999999999999999998+99/file1.txt', + 'size': 0 + } + ]}}, + 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main', + 'arv:debug': True, + 'arv:enable_reuse': True, + 'arv:on_error': 'continue' }, - 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [ - {'basename': 'renamed.txt', - 'class': 'File', - 'location': 'keep:99999999999999999999999999999998+99/file1.txt', - 'size': 0 - } - ]} - }, - 'kind': 'json' + 'repository': 'arvados', + 'script_version': 'master', + 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9', + 'script': 'cwl-runner', + 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'} + } } - }, - 'secret_mounts': {}, - 'state': 'Committed', - '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', '--on-error=continue', - '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], - 'name': 'submit_wf.cwl', - 'container_image': '999999999999999999999999999999d3+99', - 'output_path': '/var/spool/cwl', - 'cwd': '/var/spool/cwl', - 'runtime_constraints': { - 'API': True, - 'vcpus': 1, - 'ram': (1024+256)*1024*1024 - }, - 'use_existing': False, - 'properties': {}, - 'secret_mounts': {} - } + } + stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance) + stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz" + stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid + stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create) + stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = { + "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz", + "state": "Queued" + } + stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create + stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job - stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz" - stubs.api.workflows().create().execute.return_value = { - "uuid": stubs.expect_workflow_uuid, - } - def update_mock(**kwargs): - stubs.updated_uuid = kwargs.get('uuid') - return mock.DEFAULT - stubs.api.workflows().update.side_effect = update_mock - stubs.api.workflows().update().execute.side_effect = lambda **kwargs: { - "uuid": stubs.updated_uuid, - } + cwd = os.getcwd() + filepath = os.path.join(cwd, "tests/wf/submit_wf_packed.cwl") + with open(filepath) as f: + expect_packed_workflow = yaml.round_trip_load(f) + + if wfpath is None: + wfpath = wfname + + gitinfo_workflow = copy.deepcopy(expect_packed_workflow) + gitinfo_workflow["$graph"][0]["id"] = "file://%s/tests/wf/%s" % (cwd, wfpath) + mocktool = mock.NonCallableMock(tool=gitinfo_workflow["$graph"][0], metadata=gitinfo_workflow) + + git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool) + expect_packed_workflow.update(git_info) + + git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in git_info.items()} + + if wfname == wfpath: + container_name = "%s (%s)" % (wfpath, git_props["arv:gitDescribe"]) + else: + container_name = wfname + + stubs.expect_container_spec = { + 'priority': 500, + 'mounts': { + '/var/spool/cwl': { + 'writable': True, + 'kind': 'collection' + }, + '/var/lib/cwl/workflow.json': { + 'content': expect_packed_workflow, + 'kind': 'json' + }, + 'stdout': { + 'path': '/var/spool/cwl/cwl.output.json', + 'kind': 'file' + }, + '/var/lib/cwl/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:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt', + "size": 16 + }, + 'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [ + {'basename': 'renamed.txt', + 'class': 'File', + 'location': 'keep:99999999999999999999999999999998+99/file1.txt', + 'size': 0 + } + ]} + }, + 'kind': 'json' + } + }, + 'secret_mounts': {}, + 'state': 'Committed', + '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", + '--output-name=Output from workflow '+container_name, + '--debug', '--on-error=continue', + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], + 'name': container_name, + 'container_image': '999999999999999999999999999999d3+99', + 'output_name': 'Output from workflow %s' % (container_name), + 'output_path': '/var/spool/cwl', + 'cwd': '/var/spool/cwl', + 'runtime_constraints': { + 'API': True, + 'vcpus': 1, + 'ram': (1024+256)*1024*1024 + }, + 'use_existing': False, + 'properties': git_props, + 'secret_mounts': {} + } - return func(self, stubs, *args, **kwargs) - return wrapped + stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz" + stubs.api.workflows().create().execute.return_value = { + "uuid": stubs.expect_workflow_uuid, + } + def update_mock(**kwargs): + stubs.updated_uuid = kwargs.get('uuid') + return mock.DEFAULT + stubs.api.workflows().update.side_effect = update_mock + stubs.api.workflows().update().execute.side_effect = lambda **kwargs: { + "uuid": stubs.updated_uuid, + } + return func(self, stubs, *args, **kwargs) + return wrapped + return outer_wrapper class TestSubmit(unittest.TestCase): @@ -348,9 +385,15 @@ class TestSubmit(unittest.TestCase): cwltool.process._names = set() arvados_cwl.arvdocker.arv_docker_clear_cache() + def tearDown(self): + root_logger = logging.getLogger('') + + # Remove existing RuntimeStatusLoggingHandlers if they exist + handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)] + root_logger.handlers = handlers @mock.patch("time.sleep") - @stubs + @stubs() def test_submit_invalid_runner_ram(self, stubs, tm): exited = arvados_cwl.main( ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048", @@ -359,7 +402,7 @@ class TestSubmit(unittest.TestCase): self.assertEqual(exited, 1) - @stubs + @stubs() def test_submit_container(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -389,7 +432,7 @@ class TestSubmit(unittest.TestCase): self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_tool(self, stubs): # test for issue #16139 exited = arvados_cwl.main( @@ -401,7 +444,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_no_reuse(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse", @@ -414,6 +457,7 @@ class TestSubmit(unittest.TestCase): '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--disable-reuse', "--collection-cache-size=256", + "--output-name=Output from workflow submit_wf.cwl", '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] expect_container["use_existing"] = False @@ -424,7 +468,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs(('submit_wf_no_reuse.cwl', None)) def test_submit_container_reuse_disabled_by_workflow(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -433,14 +477,8 @@ class TestSubmit(unittest.TestCase): self.assertEqual(exited, 0) 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', - '--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', - '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] + expect_container["command"] = ["--disable-reuse" if v == "--enable-reuse" else v for v in expect_container["command"]] expect_container["use_existing"] = False - expect_container["name"] = "submit_wf_no_reuse.cwl" expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [ { "class": "http://arvados.org/cwl#ReuseRequirement", @@ -458,7 +496,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') - @stubs + @stubs() def test_submit_container_on_error(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop", @@ -470,6 +508,7 @@ class TestSubmit(unittest.TestCase): '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", + "--output-name=Output from workflow submit_wf.cwl", '--debug', '--on-error=stop', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -479,7 +518,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_output_name(self, stubs): output_name = "test_output_name" @@ -503,7 +542,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_storage_classes(self, stubs): exited = arvados_cwl.main( ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo", @@ -514,7 +553,9 @@ class TestSubmit(unittest.TestCase): 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", + '--enable-reuse', "--collection-cache-size=256", + '--output-name=Output from workflow submit_wf.cwl', + "--debug", "--storage-classes=foo", '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -524,7 +565,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @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", @@ -535,7 +576,9 @@ class TestSubmit(unittest.TestCase): 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", + '--enable-reuse', "--collection-cache-size=256", + "--output-name=Output from workflow submit_wf.cwl", + "--debug", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -548,13 +591,13 @@ class TestSubmit(unittest.TestCase): @mock.patch("cwltool.task_queue.TaskQueue") @mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job") @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection") - @stubs + @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") + output_callback({"out": "zzzzz"}, "success") return [] job.side_effect = set_final_output @@ -563,20 +606,20 @@ class TestSubmit(unittest.TestCase): "tests/wf/submit_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_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') + make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"}) 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 + @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) stubs.api.config().get.return_value = {"default": {"Default": True}} def set_final_output(job_order, output_callback, runtimeContext): - output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success") + output_callback({"out": "zzzzz"}, "success") return [] job.side_effect = set_final_output @@ -585,19 +628,19 @@ class TestSubmit(unittest.TestCase): "tests/wf/submit_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_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz') + make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"}) 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 + @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") + output_callback({"out": "zzzzz"}, "success") return [] job.side_effect = set_final_output @@ -606,10 +649,10 @@ class TestSubmit(unittest.TestCase): "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') + make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"}) self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_output_ttl(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600", @@ -620,7 +663,8 @@ class TestSubmit(unittest.TestCase): 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', + '--enable-reuse', "--collection-cache-size=256", + "--output-name=Output from workflow submit_wf.cwl", '--debug', '--on-error=continue', "--intermediate-output-ttl=3600", '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -631,7 +675,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_trash_intermediate(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate", @@ -654,7 +698,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_output_tags(self, stubs): output_tags = "tag0,tag1,tag2" @@ -668,6 +712,7 @@ class TestSubmit(unittest.TestCase): '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", + "--output-name=Output from workflow submit_wf.cwl", "--output-tags="+output_tags, '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -677,7 +722,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_runner_ram(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048", @@ -695,7 +740,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("arvados.collection.CollectionReader") @mock.patch("time.sleep") - @stubs + @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") @@ -707,7 +752,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("arvados.collection.CollectionReader") @mock.patch("time.sleep") - @stubs + @stubs() def test_submit_keepref(self, stubs, tm, reader): with open("tests/wf/expect_arvworkflow.cwl") as f: reader().open().__enter__().read.return_value = f.read() @@ -741,11 +786,14 @@ class TestSubmit(unittest.TestCase): }, 'state': 'Committed', 'output_path': '/var/spool/cwl', 'name': 'expect_arvworkflow.cwl#main', + 'output_name': 'Output from workflow expect_arvworkflow.cwl#main', 'container_image': '999999999999999999999999999999d3+99', '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', '--on-error=continue', + '--enable-reuse', "--collection-cache-size=256", + '--output-name=Output from workflow expect_arvworkflow.cwl#main', + '--debug', '--on-error=continue', '/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'], 'cwd': '/var/spool/cwl', 'runtime_constraints': { @@ -765,7 +813,7 @@ class TestSubmit(unittest.TestCase): self.assertEqual(exited, 0) @mock.patch("time.sleep") - @stubs + @stubs() def test_submit_arvworkflow(self, stubs, tm): with open("tests/wf/expect_arvworkflow.cwl") as f: stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"} @@ -861,7 +909,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs(('hello container 123', 'submit_wf.cwl')) def test_submit_container_name(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123", @@ -869,7 +917,6 @@ class TestSubmit(unittest.TestCase): stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) 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)) @@ -877,7 +924,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_missing_input(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -891,7 +938,7 @@ class TestSubmit(unittest.TestCase): stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 1) - @stubs + @stubs() def test_submit_container_project(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} @@ -905,7 +952,8 @@ class TestSubmit(unittest.TestCase): 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', + '--enable-reuse', "--collection-cache-size=256", + "--output-name=Output from workflow submit_wf.cwl", '--debug', '--on-error=continue', '--project-uuid='+project_uuid, '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -916,7 +964,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_eval_timeout(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60", @@ -937,7 +985,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_collection_cache(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500", @@ -959,7 +1007,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_thread_count(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20", @@ -980,7 +1028,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_runner_image(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123", @@ -996,7 +1044,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_priority(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669", @@ -1012,7 +1060,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs(('submit_wf_runner_resources.cwl', None)) def test_submit_wf_runner_resources(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -1025,7 +1073,6 @@ class TestSubmit(unittest.TestCase): "vcpus": 2, "ram": (2000+512) * 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", @@ -1037,11 +1084,7 @@ class TestSubmit(unittest.TestCase): expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = { "arv": "http://arvados.org/cwl#", } - 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=512", '--debug', '--on-error=continue', - '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] + expect_container["command"] = ["--collection-cache-size=512" if v == "--collection-cache-size=256" else v for v in expect_container["command"]] stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) @@ -1049,9 +1092,6 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - 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") @@ -1069,6 +1109,18 @@ class TestSubmit(unittest.TestCase): "name": "arvados/jobs:"+arvados_cwl.__version__, "owner_uuid": "", "properties": {"image_timestamp": ""}}], "items_available": 1, "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": [{"created_at": "", + "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb", + "link_class": "docker_image_repo+tag", + "name": "arvados/jobs:"+arvados_cwl.__version__, + "owner_uuid": "", + "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}, {"items": [{"created_at": "", "head_uuid": "", "link_class": "docker_image_hash", @@ -1082,15 +1134,21 @@ class TestSubmit(unittest.TestCase): "owner_uuid": "", "manifest_text": "", "properties": "" - }], "items_available": 1, "offset": 0},) + }], "items_available": 1, "offset": 0}, + {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb", + "owner_uuid": "", + "manifest_text": "", + "properties": "" + }], "items_available": 1, "offset": 0}) arvrunner.api.collections().create().execute.return_value = {"uuid": ""} 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__)) + arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__, arvrunner.runtimeContext)) - @stubs + @stubs() def test_submit_secrets(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -1109,6 +1167,7 @@ class TestSubmit(unittest.TestCase): '--thread-count=0', "--enable-reuse", "--collection-cache-size=256", + '--output-name=Output from workflow secret_wf.cwl' '--debug', "--on-error=continue", "/var/lib/cwl/workflow.json#main", @@ -1234,6 +1293,7 @@ class TestSubmit(unittest.TestCase): } }, "name": "secret_wf.cwl", + "output_name": "Output from workflow secret_wf.cwl", "output_path": "/var/spool/cwl", "priority": 500, "properties": {}, @@ -1258,7 +1318,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_request_uuid(self, stubs): stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123" stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy" @@ -1280,7 +1340,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_container_cluster_id(self, stubs): stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123" @@ -1297,7 +1357,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_validate_cluster_id(self, stubs): stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123" exited = arvados_cwl.main( @@ -1306,7 +1366,7 @@ class TestSubmit(unittest.TestCase): stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) self.assertEqual(exited, 1) - @stubs + @stubs() def test_submit_validate_project_uuid(self, stubs): # Fails with bad cluster prefix exited = arvados_cwl.main( @@ -1332,7 +1392,7 @@ class TestSubmit(unittest.TestCase): @mock.patch("arvados.collection.CollectionReader") - @stubs + @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") @@ -1367,7 +1427,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_mismatched_uuid_inputs(self, stubs): def list_side_effect(**kwargs): m = mock.MagicMock() @@ -1400,7 +1460,7 @@ class TestSubmit(unittest.TestCase): cwltool_logger.removeHandler(stderr_logger) @mock.patch("arvados.collection.CollectionReader") - @stubs + @stubs() def test_submit_unknown_uuid_inputs(self, stubs, collectionReader): collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt") capture_stderr = StringIO() @@ -1418,11 +1478,11 @@ class TestSubmit(unittest.TestCase): self.assertEqual(exited, 1) self.assertRegex( capture_stderr.getvalue(), - r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found") + r"Collection\s*uuid\s*zzzzz-4zz18-zzzzzzzzzzzzzzz\s*not\s*found") finally: cwltool_logger.removeHandler(stderr_logger) - @stubs + @stubs(('submit_wf_process_properties.cwl', None)) def test_submit_set_process_properties(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -1430,7 +1490,7 @@ class TestSubmit(unittest.TestCase): stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) expect_container = copy.deepcopy(stubs.expect_container_spec) - expect_container["name"] = "submit_wf_process_properties.cwl" + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [ { "class": "http://arvados.org/cwl#ProcessProperties", @@ -1452,14 +1512,14 @@ class TestSubmit(unittest.TestCase): "arv": "http://arvados.org/cwl#" } - expect_container["properties"] = { + expect_container["properties"].update({ "baz": "blorp.txt", "foo": "bar", "quux": { "q1": 1, "q2": 2 } - } + }) stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) @@ -1468,7 +1528,7 @@ class TestSubmit(unittest.TestCase): self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_enable_preemptible(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible", @@ -1489,7 +1549,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_disable_preemptible(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible", @@ -1520,7 +1580,14 @@ class TestCreateWorkflow(unittest.TestCase): cwltool.process._names = set() arvados_cwl.arvdocker.arv_docker_clear_cache() - @stubs + def tearDown(self): + root_logger = logging.getLogger('') + + # Remove existing RuntimeStatusLoggingHandlers if they exist + handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)] + root_logger.handlers = handlers + + @stubs() def test_create(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} @@ -1550,7 +1617,7 @@ class TestCreateWorkflow(unittest.TestCase): stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_create_name(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} @@ -1582,8 +1649,11 @@ class TestCreateWorkflow(unittest.TestCase): self.assertEqual(exited, 0) - @stubs + @stubs() def test_update(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid} + exited = arvados_cwl.main( ["--update-workflow", self.existing_workflow_uuid, "--debug", @@ -1595,6 +1665,7 @@ class TestCreateWorkflow(unittest.TestCase): "name": "submit_wf.cwl", "description": "", "definition": self.expect_workflow, + "owner_uuid": project_uuid } } stubs.api.workflows().update.assert_called_with( @@ -1604,8 +1675,12 @@ class TestCreateWorkflow(unittest.TestCase): self.existing_workflow_uuid + '\n') self.assertEqual(exited, 0) - @stubs + + @stubs() def test_update_name(self, stubs): + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid} + exited = arvados_cwl.main( ["--update-workflow", self.existing_workflow_uuid, "--debug", "--name", "testing 123", @@ -1617,6 +1692,7 @@ class TestCreateWorkflow(unittest.TestCase): "name": "testing 123", "description": "", "definition": self.expect_workflow, + "owner_uuid": project_uuid } } stubs.api.workflows().update.assert_called_with( @@ -1626,7 +1702,7 @@ class TestCreateWorkflow(unittest.TestCase): self.existing_workflow_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_create_collection_per_tool(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} @@ -1656,7 +1732,7 @@ class TestCreateWorkflow(unittest.TestCase): stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_create_with_imports(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} @@ -1675,7 +1751,7 @@ class TestCreateWorkflow(unittest.TestCase): stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_create_with_no_input(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"}