X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/02e05f2d3f790877158fa2ae5d9ceaa7e26f22fc..37516bc14fdfe634c78764c15f3a8eb3a09b403c:/sdk/cwl/tests/test_submit.py diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py index adee2d2089..c8bf127951 100644 --- a/sdk/cwl/tests/test_submit.py +++ b/sdk/cwl/tests/test_submit.py @@ -10,6 +10,7 @@ from future.utils import viewvalues import copy import io +import itertools import functools import hashlib import json @@ -19,6 +20,7 @@ import sys import unittest import cwltool.process import re +import os from io import BytesIO @@ -41,312 +43,267 @@ import arvados.keep from .matcher import JsonDiffMatcher, StripYAMLComments from .mock_discovery import get_rootDesc -import ruamel.yaml as yaml +import ruamel.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", + "df80736f-f14d-4b10-b2e3-03aa27f034b6", "df80736f-f14d-4b10-b2e3-03aa27f034b7", + "df80736f-f14d-4b10-b2e3-03aa27f034b8", "df80736f-f14d-4b10-b2e3-03aa27f034b9", + "df80736f-f14d-4b10-b2e3-03aa27f034c0", "df80736f-f14d-4b10-b2e3-03aa27f034c1", + "df80736f-f14d-4b10-b2e3-03aa27f034c2", "df80736f-f14d-4b10-b2e3-03aa27f034c3", + "df80736f-f14d-4b10-b2e3-03aa27f034c4", "df80736f-f14d-4b10-b2e3-03aa27f034c5", + "df80736f-f14d-4b10-b2e3-03aa27f034c6", "df80736f-f14d-4b10-b2e3-03aa27f034c7"] + + 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 - } - }.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') + stubs.api.users().current().execute.return_value = { + "uuid": stubs.fake_user_uuid, } - 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_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" + } - with open("tests/wf/submit_wf_packed.cwl") as f: - expect_packed_workflow = yaml.round_trip_load(f) + cwd = os.getcwd() + filepath = os.path.join(cwd, "tests/wf/submit_wf_wrapper.cwl") + with open(filepath) as f: + yaml = ruamel.yaml.YAML(typ='rt', pure=True) + expect_packed_workflow = yaml.load(f) - 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' + 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) + + stubs.git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool) + expect_packed_workflow.update(stubs.git_info) + + stubs.git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in stubs.git_info.items()} + + step_name = "%s (%s)" % (wfpath, stubs.git_props["arv:gitDescribe"]) + if wfname == wfpath: + container_name = "%s (%s)" % (wfpath, stubs.git_props["arv:gitDescribe"]) + else: + container_name = wfname + + expect_packed_workflow["$graph"][0]["steps"][0]["id"] = "#main/"+step_name + expect_packed_workflow["$graph"][0]["steps"][0]["label"] = container_name + + 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' + } }, - 'stdout': { - 'path': '/var/spool/cwl/cwl.output.json', - 'kind': 'file' + '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 }, - '/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", '--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.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, - } + 'properties': stubs.git_props, + 'use_existing': False, + '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): def setUp(self): cwltool.process._names = set() - arvados_cwl.arvdocker.arv_docker_clear_cache() + #arvados_cwl.arvdocker.arv_docker_clear_cache() def tearDown(self): root_logger = logging.getLogger('') @@ -356,7 +313,7 @@ class TestSubmit(unittest.TestCase): 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", @@ -365,7 +322,7 @@ 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", @@ -377,7 +334,7 @@ class TestSubmit(unittest.TestCase): 'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n', 'replication_desired': None, - 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)', + 'name': 'submit_wf.cwl ('+ stubs.git_props["arv:gitDescribe"] +') input (169f39d466a5438ac4a90e779bf750c7+53)', }), ensure_unique_name=False), mock.call(body=JsonDiffMatcher({ 'manifest_text': @@ -395,7 +352,7 @@ 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( @@ -407,7 +364,7 @@ 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", @@ -420,6 +377,7 @@ 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 (%s)' % stubs.git_props["arv:gitDescribe"], '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] expect_container["use_existing"] = False @@ -430,7 +388,7 @@ 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", @@ -439,24 +397,19 @@ 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"]["$graph"][1]["hints"] = [ + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [ { - "class": "http://arvados.org/cwl#ReuseRequirement", + "class": "WorkReuse", "enableReuse": False, }, + { + "acrContainerImage": "999999999999999999999999999999d3+99", + "class": "http://arvados.org/cwl#WorkflowRunnerResources" + } ] - expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = { - "arv": "http://arvados.org/cwl#", - "cwltool": "http://commonwl.org/cwltool#" - } + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:fa5fbf21deb74f9f239daa3f5bb4b902+292/wf/submit_wf_no_reuse.cwl" stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) @@ -464,7 +417,7 @@ 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", @@ -476,6 +429,7 @@ 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 (%s)' % stubs.git_props["arv:gitDescribe"], '--debug', '--on-error=stop', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -485,7 +439,7 @@ 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" @@ -509,7 +463,7 @@ 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", @@ -520,7 +474,9 @@ 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 (%s)' % stubs.git_props["arv:gitDescribe"], + "--debug", "--storage-classes=foo", '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -530,7 +486,7 @@ 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", @@ -541,7 +497,9 @@ 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 (%s)' % stubs.git_props["arv:gitDescribe"], + "--debug", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -554,68 +512,68 @@ 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 exited = arvados_cwl.main( - ["--debug", "--local", "--storage-classes=foo", + ["--debug", "--local", "--storage-classes=foo", "--disable-git", "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 from workflow 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 exited = arvados_cwl.main( - ["--debug", "--local", + ["--debug", "--local", "--disable-git", "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 from workflow 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 exited = arvados_cwl.main( - ["--debug", "--local", + ["--debug", "--local", "--disable-git", "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 from workflow 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", @@ -626,7 +584,9 @@ 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 (%s)' % stubs.git_props["arv:gitDescribe"], + '--debug', '--on-error=continue', "--intermediate-output-ttl=3600", '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -637,7 +597,7 @@ 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", @@ -650,6 +610,7 @@ 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 (%s)' % stubs.git_props["arv:gitDescribe"], '--debug', '--on-error=continue', "--trash-intermediate", '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -660,7 +621,7 @@ 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" @@ -674,6 +635,7 @@ 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 (%s)' % stubs.git_props["arv:gitDescribe"], "--output-tags="+output_tags, '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -683,7 +645,7 @@ 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", @@ -692,6 +654,13 @@ class TestSubmit(unittest.TestCase): expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024 + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [ + { + "acrContainerImage": "999999999999999999999999999999d3+99", + "class": "http://arvados.org/cwl#WorkflowRunnerResources", + "ramMin": 2048 + } + ] stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) @@ -701,7 +670,7 @@ 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") @@ -713,7 +682,7 @@ 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() @@ -747,11 +716,14 @@ 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': { @@ -771,13 +743,13 @@ 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"} exited = arvados_cwl.main( - ["--submit", "--no-wait", "--api=containers", "--debug", + ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-git", "962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) @@ -796,6 +768,7 @@ class TestSubmit(unittest.TestCase): 'kind': 'json', 'content': { 'cwlVersion': 'v1.0', + 'label': 'a test workflow', '$graph': [ { 'id': '#main', @@ -821,8 +794,7 @@ class TestSubmit(unittest.TestCase): 'requirements': [ { 'dockerPull': 'debian:buster-slim', - 'class': 'DockerRequirement', - "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" + 'class': 'DockerRequirement' } ], 'id': '#submit_tool.cwl', @@ -846,8 +818,11 @@ class TestSubmit(unittest.TestCase): '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 a test workflow", + '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'], + 'output_name': 'Output from workflow a test workflow', 'cwd': '/var/spool/cwl', 'runtime_constraints': { 'API': True, @@ -867,7 +842,7 @@ 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", @@ -875,7 +850,6 @@ 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)) @@ -883,7 +857,7 @@ 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", @@ -897,7 +871,7 @@ 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"} @@ -911,7 +885,9 @@ 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 (%s)' % stubs.git_props["arv:gitDescribe"], + '--debug', '--on-error=continue', '--project-uuid='+project_uuid, '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -922,7 +898,7 @@ 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", @@ -934,6 +910,7 @@ class TestSubmit(unittest.TestCase): '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=60.0', '--thread-count=0', '--enable-reuse', "--collection-cache-size=256", + '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"], '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -943,7 +920,7 @@ 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", @@ -955,6 +932,7 @@ class TestSubmit(unittest.TestCase): '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=0', '--enable-reuse', "--collection-cache-size=500", + '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"], '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024 @@ -965,7 +943,7 @@ 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", @@ -977,6 +955,7 @@ class TestSubmit(unittest.TestCase): '--no-log-timestamps', '--disable-validate', '--disable-color', '--eval-timeout=20', '--thread-count=20', '--enable-reuse', "--collection-cache-size=256", + '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"], '--debug', '--on-error=continue', '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] @@ -986,7 +965,7 @@ 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", @@ -994,6 +973,12 @@ class TestSubmit(unittest.TestCase): stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99" + stubs.expect_container_spec["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [ + { + "acrContainerImage": "999999999999999999999999999999d5+99", + "class": "http://arvados.org/cwl#WorkflowRunnerResources" + } + ] expect_container = copy.deepcopy(stubs.expect_container_spec) stubs.api.container_requests().create.assert_called_with( @@ -1002,7 +987,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs() def test_submit_priority(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669", @@ -1018,7 +1003,7 @@ class TestSubmit(unittest.TestCase): stubs.expect_container_request_uuid + '\n') self.assertEqual(exited, 0) - @stubs + @stubs(('submit_wf_runner_resources.cwl', None)) def test_submit_wf_runner_resources(self, stubs): exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -1031,23 +1016,20 @@ class TestSubmit(unittest.TestCase): "vcpus": 2, "ram": (2000+512) * 2**20 } - expect_container["name"] = "submit_wf_runner_resources.cwl" - expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [ + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [ { "class": "http://arvados.org/cwl#WorkflowRunnerResources", + "acrContainerImage": "999999999999999999999999999999d3+99", "coresMin": 2, "ramMin": 2000, "keep_cache": 512 } ] - expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$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["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = { + # "arv": "http://arvados.org/cwl#", + #} + expect_container["command"] = ["--collection-cache-size=512" if v == "--collection-cache-size=256" else v for v in expect_container["command"]] + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:80b60e39456505b91d3989a1f5058b98+308/wf/submit_wf_runner_resources.cwl" stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) @@ -1059,47 +1041,62 @@ class TestSubmit(unittest.TestCase): @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() + #arvados_cwl.arvdocker.arv_docker_clear_cache() arvrunner = mock.MagicMock() arvrunner.project_uuid = "" api.return_value = mock.MagicMock() arvrunner.api = api.return_value arvrunner.runtimeContext.match_local_docker = False - 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": "", - "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} - ) + arvrunner.api.links().list().execute.side_effect = itertools.cycle([ + {"items": [{"created_at": "2023-08-25T12:34:56.123456Z", + "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb", + "link_class": "docker_image_repo+tag", + "name": "arvados/jobs:"+arvados_cwl.__version__, + "owner_uuid": "", + "uuid": "zzzzz-o0j2j-arvadosjobsrepo", + "properties": {"image_timestamp": ""}}]}, + {"items": []}, + {"items": []}, + {"items": [{"created_at": "2023-08-25T12:34:57.234567Z", + "head_uuid": "", + "link_class": "docker_image_hash", + "name": "123456", + "owner_uuid": "", + "uuid": "zzzzz-o0j2j-arvadosjobshash", + "properties": {"image_timestamp": ""}}]}, + {"items": []}, + {"items": []}, + ]) find_one_image_hash.return_value = "123456" - arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb", - "owner_uuid": "", - "manifest_text": "", - "properties": "" - }], "items_available": 1, "offset": 0},) + arvrunner.api.collections().list().execute.side_effect = itertools.cycle([ + {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb", + "owner_uuid": "", + "manifest_text": "", + "created_at": "2023-08-25T12:34:55.012345Z", + "properties": {}}]}, + {"items": []}, + {"items": []}, + ]) 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", + ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-git", "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"], stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + stubs.git_props["arv:gitPath"] = "sdk/cwl/tests/wf/secret_wf.cwl" + stubs.git_info["http://arvados.org/cwl#gitPath"] = "sdk/cwl/tests/wf/secret_wf.cwl" + expect_container = { "command": [ "arvados-cwl-runner", @@ -1112,7 +1109,8 @@ class TestSubmit(unittest.TestCase): '--thread-count=0', "--enable-reuse", "--collection-cache-size=256", - '--debug', + "--output-name=Output from workflow secret_wf.cwl", + "--debug", "--on-error=continue", "/var/lib/cwl/workflow.json#main", "/var/lib/cwl/cwl.input.json" @@ -1131,62 +1129,23 @@ class TestSubmit(unittest.TestCase): "/var/lib/cwl/workflow.json": { "content": { "$graph": [ - { - "arguments": [ - "md5sum", - "example.conf" - ], - "class": "CommandLineTool", - "hints": [ - { - "class": "http://commonwl.org/cwltool#Secrets", - "secrets": [ - "#secret_job.cwl/pw" - ] - } - ], - "id": "#secret_job.cwl", - "inputs": [ - { - "id": "#secret_job.cwl/pw", - "type": "string" - } - ], - "outputs": [ - { - "id": "#secret_job.cwl/out", - "type": "File", - "outputBinding": { - "glob": "hashed_example.txt" - } - } - ], - "stdout": "hashed_example.txt", - "requirements": [ - { - "class": "InitialWorkDirRequirement", - "listing": [ - { - "entry": "username: user\npassword: $(inputs.pw)\n", - "entryname": "example.conf" - } - ] - } - ] - }, { "class": "Workflow", "hints": [ { - "class": "DockerRequirement", - "dockerPull": "debian:buster-slim", - "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" + "class": "DockerRequirement", + "dockerPull": "debian:buster-slim", + "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99" }, { "class": "http://commonwl.org/cwltool#Secrets", "secrets": [ "#main/pw" ] + }, + { + "acrContainerImage": "999999999999999999999999999999d3+99", + "class": "http://arvados.org/cwl#WorkflowRunnerResources" } ], "id": "#main", @@ -1199,31 +1158,34 @@ class TestSubmit(unittest.TestCase): "outputs": [ { "id": "#main/out", - "outputSource": "#main/step1/out", + "outputSource": "#main/step/out", "type": "File" } ], + "requirements": [ + { + "class": "SubworkflowFeatureRequirement" + } + ], "steps": [ { - "id": "#main/step1", + "id": "#main/secret_wf.cwl", "in": [ { - "id": "#main/step1/pw", + "id": "#main/step/pw", "source": "#main/pw" } ], + "label": "secret_wf.cwl", "out": [ - "#main/step1/out" + {"id": "#main/step/out"} ], - "run": "#secret_job.cwl" + "run": "keep:991302581d01db470345a131480e623b+247/secret_wf.cwl" } ] } ], - "$namespaces": { - "cwltool": "http://commonwl.org/cwltool#" - }, - "cwlVersion": "v1.0" + "cwlVersion": "v1.2" }, "kind": "json" }, @@ -1237,6 +1199,7 @@ class TestSubmit(unittest.TestCase): } }, "name": "secret_wf.cwl", + "output_name": "Output from workflow secret_wf.cwl", "output_path": "/var/spool/cwl", "priority": 500, "properties": {}, @@ -1261,7 +1224,7 @@ 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" @@ -1283,7 +1246,7 @@ 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" @@ -1300,7 +1263,7 @@ 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( @@ -1309,7 +1272,7 @@ 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( @@ -1335,7 +1298,7 @@ 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") @@ -1349,6 +1312,7 @@ class TestSubmit(unittest.TestCase): m.execute.return_value = {"items": []} return m stubs.api.collections().list.side_effect = list_side_effect + collectionReader().portable_data_hash.return_value = "99999999999999999999999999999998+99" exited = arvados_cwl.main( ["--submit", "--no-wait", "--api=containers", "--debug", @@ -1370,7 +1334,7 @@ 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() @@ -1403,7 +1367,7 @@ 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() @@ -1425,7 +1389,7 @@ class TestSubmit(unittest.TestCase): 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", @@ -1433,8 +1397,8 @@ 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"]["$graph"][1]["hints"] = [ + + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [ { "class": "http://arvados.org/cwl#ProcessProperties", "processProperties": [ @@ -1449,20 +1413,26 @@ class TestSubmit(unittest.TestCase): } } ], + }, + { + "acrContainerImage": "999999999999999999999999999999d3+99", + "class": "http://arvados.org/cwl#WorkflowRunnerResources" } ] - expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = { - "arv": "http://arvados.org/cwl#" - } + #expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = { + # "arv": "http://arvados.org/cwl#" + #} - expect_container["properties"] = { + expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:df44f9dd4b9467159f210f967e45417f+312/wf/submit_wf_process_properties.cwl" + + 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)) @@ -1471,7 +1441,7 @@ 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", @@ -1480,11 +1450,13 @@ class TestSubmit(unittest.TestCase): expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers', - '--no-log-timestamps', '--disable-validate', '--disable-color', - '--eval-timeout=20', '--thread-count=0', - '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', + '--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 (%s)' % stubs.git_props["arv:gitDescribe"], + '--debug', '--on-error=continue', '--enable-preemptible', - '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) @@ -1492,7 +1464,7 @@ 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", @@ -1501,11 +1473,57 @@ class TestSubmit(unittest.TestCase): expect_container = copy.deepcopy(stubs.expect_container_spec) expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers', - '--no-log-timestamps', '--disable-validate', '--disable-color', - '--eval-timeout=20', '--thread-count=0', - '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue', + '--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 (%s)' % stubs.git_props["arv:gitDescribe"], + '--debug', '--on-error=continue', '--disable-preemptible', - '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] + + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(expect_container)) + self.assertEqual(stubs.capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + self.assertEqual(exited, 0) + + @stubs() + def test_submit_container_prefer_cached_downloads(self, stubs): + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--prefer-cached-downloads", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + + expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', + '--enable-reuse', "--collection-cache-size=256", + '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"], + '--debug', "--on-error=continue", '--prefer-cached-downloads', + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] + + stubs.api.container_requests().create.assert_called_with( + body=JsonDiffMatcher(expect_container)) + self.assertEqual(stubs.capture_stdout.getvalue(), + stubs.expect_container_request_uuid + '\n') + self.assertEqual(exited, 0) + + @stubs() + def test_submit_container_varying_url_params(self, stubs): + exited = arvados_cwl.main( + ["--submit", "--no-wait", "--api=containers", "--debug", "--varying-url-params", "KeyId,Signature", + "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client) + + expect_container = copy.deepcopy(stubs.expect_container_spec) + expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers', + '--no-log-timestamps', '--disable-validate', '--disable-color', + '--eval-timeout=20', '--thread-count=0', + '--enable-reuse', "--collection-cache-size=256", + '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"], + '--debug', "--on-error=continue", "--varying-url-params=KeyId,Signature", + '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'] stubs.api.container_requests().create.assert_called_with( body=JsonDiffMatcher(expect_container)) @@ -1517,11 +1535,13 @@ class TestSubmit(unittest.TestCase): class TestCreateWorkflow(unittest.TestCase): existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml" expect_workflow = StripYAMLComments( - open("tests/wf/expect_upload_packed.cwl").read().rstrip()) + open("tests/wf/expect_upload_wrapper.cwl").read().rstrip()) + expect_workflow_altname = StripYAMLComments( + open("tests/wf/expect_upload_wrapper_altname.cwl").read().rstrip()) def setUp(self): cwltool.process._names = set() - arvados_cwl.arvdocker.arv_docker_clear_cache() + #arvados_cwl.arvdocker.arv_docker_clear_cache() def tearDown(self): root_logger = logging.getLogger('') @@ -1530,7 +1550,7 @@ class TestCreateWorkflow(unittest.TestCase): handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)] root_logger.handlers = handlers - @stubs + @stubs() def test_create(self, stubs): project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' stubs.api.groups().get().execute.return_value = {"group_class": "project"} @@ -1539,6 +1559,7 @@ class TestCreateWorkflow(unittest.TestCase): ["--create-workflow", "--debug", "--api=containers", "--project-uuid", project_uuid, + "--disable-git", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) @@ -1560,7 +1581,7 @@ 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"} @@ -1570,6 +1591,7 @@ class TestCreateWorkflow(unittest.TestCase): "--api=containers", "--project-uuid", project_uuid, "--name", "testing 123", + "--disable-git", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) @@ -1581,7 +1603,7 @@ class TestCreateWorkflow(unittest.TestCase): "owner_uuid": project_uuid, "name": "testing 123", "description": "", - "definition": self.expect_workflow, + "definition": self.expect_workflow_altname, } } stubs.api.workflows().create.assert_called_with( @@ -1592,11 +1614,15 @@ 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", + "--disable-git", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) @@ -1605,6 +1631,7 @@ class TestCreateWorkflow(unittest.TestCase): "name": "submit_wf.cwl", "description": "", "definition": self.expect_workflow, + "owner_uuid": project_uuid } } stubs.api.workflows().update.assert_called_with( @@ -1614,11 +1641,16 @@ 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", + "--disable-git", "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) @@ -1626,7 +1658,8 @@ class TestCreateWorkflow(unittest.TestCase): "workflow": { "name": "testing 123", "description": "", - "definition": self.expect_workflow, + "definition": self.expect_workflow_altname, + "owner_uuid": project_uuid } } stubs.api.workflows().update.assert_called_with( @@ -1636,7 +1669,7 @@ 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"} @@ -1645,10 +1678,11 @@ class TestCreateWorkflow(unittest.TestCase): ["--create-workflow", "--debug", "--api=containers", "--project-uuid", project_uuid, + "--disable-git", "tests/collection_per_tool/collection_per_tool.cwl"], stubs.capture_stdout, sys.stderr, api_client=stubs.api) - toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl" + toolfile = "tests/collection_per_tool/collection_per_tool_wrapper.cwl" expect_workflow = StripYAMLComments(open(toolfile).read().rstrip()) body = { @@ -1666,7 +1700,7 @@ 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"} @@ -1685,7 +1719,7 @@ 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"} @@ -1703,3 +1737,55 @@ class TestCreateWorkflow(unittest.TestCase): self.assertEqual(stubs.capture_stdout.getvalue(), stubs.expect_workflow_uuid + '\n') self.assertEqual(exited, 0) + + @stubs() + def test_create_map(self, stubs): + # test uploading a document that uses objects instead of arrays + # for certain fields like inputs and requirements. + + project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz' + stubs.api.groups().get().execute.return_value = {"group_class": "project"} + + exited = arvados_cwl.main( + ["--create-workflow", "--debug", + "--api=containers", + "--project-uuid", project_uuid, + "--disable-git", + "tests/wf/submit_wf_map.cwl", "tests/submit_test_job.json"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api) + + stubs.api.pipeline_templates().create.refute_called() + stubs.api.container_requests().create.refute_called() + + expect_workflow = StripYAMLComments( + open("tests/wf/expect_upload_wrapper_map.cwl").read().rstrip()) + + body = { + "workflow": { + "owner_uuid": project_uuid, + "name": "submit_wf_map.cwl", + "description": "", + "definition": expect_workflow, + } + } + stubs.api.workflows().create.assert_called_with( + body=JsonDiffMatcher(body)) + + self.assertEqual(stubs.capture_stdout.getvalue(), + stubs.expect_workflow_uuid + '\n') + self.assertEqual(exited, 0) + + +class TestPrintKeepDeps(unittest.TestCase): + @stubs() + def test_print_keep_deps(self, stubs): + # test --print-keep-deps which is used by arv-copy + + exited = arvados_cwl.main( + ["--print-keep-deps", "--debug", + "tests/wf/submit_wf_map.cwl"], + stubs.capture_stdout, sys.stderr, api_client=stubs.api) + + self.assertEqual(stubs.capture_stdout.getvalue(), + '["5d373e7629203ce39e7c22af98a0f881+52", "999999999999999999999999999999d4+99"]' + '\n') + self.assertEqual(exited, 0)