import mock
import sys
import unittest
+import cwltool.process
+import re
-from io import BytesIO, StringIO
+from io import BytesIO
+
+# StringIO.StringIO and io.StringIO have different behavior write() is
+# called with both python2 (byte) strings and unicode strings
+# (specifically there's some logging in cwltool that causes trouble).
+# This isn't a problem on python3 because all string are unicode.
+if sys.version_info[0] < 3:
+ from StringIO import StringIO
+else:
+ from io import StringIO
import arvados
import arvados.collection
_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:8": [("zzzzz-4zz18-zzzzzzzzzzzzzd4", "")],
- "arvados/jobs:123": [("zzzzz-4zz18-zzzzzzzzzzzzzd5", "")],
- "arvados/jobs:latest": [("zzzzz-4zz18-zzzzzzzzzzzzzd6", "")],
- }
- def kd(a, b, image_name=None, image_tag=None):
- return stubs.docker_images.get("%s:%s" % (image_name, image_tag), [])
- stubs.keepdocker.side_effect = kd
-
- stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
- stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz"
+def stubs(wfname='submit_wf.cwl'):
+ 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
+ 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
- if sys.version_info[0] < 3:
- stubs.capture_stdout = BytesIO()
- else:
- stubs.capture_stdout = StringIO()
+ stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
+ stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz"
- stubs.api = mock.MagicMock()
- stubs.api._rootDesc = get_rootDesc()
+ if sys.version_info[0] < 3:
+ stubs.capture_stdout = BytesIO()
+ else:
+ stubs.capture_stdout = StringIO()
- 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 = mock.MagicMock()
+ stubs.api._rootDesc = get_rootDesc()
+ stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
+ stubs.api._rootDesc["revision"] = "20210628"
- 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"
- },
- "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)
- with open("tests/wf/submit_wf_packed.cwl") as f:
- expect_packed_workflow = yaml.round_trip_load(f)
+ stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ stubs.api.jobs().create().execute.return_value = {
+ "uuid": stubs.expect_job_uuid,
+ "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_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
},
- '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',
- '--eval-timeout=20', '--thread-count=1',
- '--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': True,
- '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,
- }
+ }
+ 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
+
+ with open("tests/wf/submit_wf_packed.cwl") as f:
+ expect_packed_workflow = yaml.round_trip_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'
+ },
+ '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 '+wfname,
+ '--debug', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
+ 'name': wfname,
+ 'container_image': '999999999999999999999999999999d3+99',
+ 'output_name': 'Output from workflow '+wfname,
+ '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': {}
+ }
- 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):
- @mock.patch("arvados_cwl.arvdocker.arv_docker_get_image")
- @mock.patch("time.sleep")
- @stubs
- def test_submit(self, stubs, tm, arvdock):
- def get_image(api_client, dockerRequirement, pull_image, project_uuid):
- if dockerRequirement["dockerPull"] == 'arvados/jobs:'+arvados_cwl.__version__:
- return '999999999999999999999999999999d3+99'
- elif dockerRequirement["dockerPull"] == "debian:8":
- return '999999999999999999999999999999d4+99'
- arvdock.side_effect = get_image
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- stubs.api.collections().create.assert_has_calls([
- mock.call(body=JsonDiffMatcher({
- 'manifest_text':
- '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
- 'replication_desired': None,
- 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
- }), ensure_unique_name=False),
- mock.call(body=JsonDiffMatcher({
- 'manifest_text':
- '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'replication_desired': None,
- 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
- }), ensure_unique_name=False),
- mock.call(body=JsonDiffMatcher({
- 'manifest_text':
- ". 68089141fbf7e020ac90a9d6a575bc8f+1312 0:1312:workflow.cwl\n",
- 'replication_desired': None,
- 'name': 'submit_wf.cwl',
- }), ensure_unique_name=True) ])
-
- arvdock.assert_has_calls([
- mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8"}, True, None),
- mock.call(stubs.api, {"class": "DockerRequirement", "dockerPull": "debian:8", 'http://arvados.org/cwl#dockerCollectionPDH': '999999999999999999999999999999d4+99'}, True, None),
- mock.call(stubs.api, {'dockerPull': 'arvados/jobs:'+arvados_cwl.__version__}, True, None)
- ])
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_no_reuse(self, stubs, tm):
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
- expect_pipeline["properties"] = {"run_options": {"enable_job_reuse": False}}
-
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
-
- @stubs
- def test_error_when_multiple_storage_classes_specified(self, stubs):
- storage_classes = "foo,bar"
- exited = arvados_cwl.main(
- ["--debug", "--storage-classes", storage_classes,
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdin, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 1)
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_on_error(self, stubs, tm):
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
-
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_runner_ram(self, stubs, tm):
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+ def setUp(self):
+ cwltool.process._names = set()
+ arvados_cwl.arvdocker.arv_docker_clear_cache()
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
+ def tearDown(self):
+ root_logger = logging.getLogger('')
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
+ # 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.capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 1)
- @mock.patch("time.sleep")
- @stubs
- def test_submit_output_name(self, stubs, tm):
- output_name = "test_output_name"
-
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug", "--output-name", output_name,
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
-
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_pipeline_name(self, stubs, tm):
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug", "--name=hello job 123",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["name"] = "hello job 123"
-
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_output_tags(self, stubs, tm):
- output_tags = "tag0,tag1,tag2"
-
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_tags"] = output_tags
-
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
-
- @mock.patch("time.sleep")
- @stubs
- def test_submit_with_project_uuid(self, stubs, tm):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
-
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug",
- "--project-uuid", project_uuid,
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["owner_uuid"] = project_uuid
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
@stubs
def test_submit_container(self, stubs):
stubs.api.collections().create.assert_has_calls([
mock.call(body=JsonDiffMatcher({
'manifest_text':
- '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
+ '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
'replication_desired': None,
- 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
+ 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
}), ensure_unique_name=False),
mock.call(body=JsonDiffMatcher({
'manifest_text':
- '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
+ '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
'replication_desired': None,
- 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
- }), ensure_unique_name=False)])
+ 'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
+ }), ensure_unique_name=False),
+ ])
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
+
+ @stubs
+ def test_submit_container_tool(self, stubs):
+ # test for issue #16139
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/tool/tool_with_sf.cwl", "tests/tool/tool_with_sf.yml"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
@stubs
def test_submit_container_no_reuse(self, stubs):
exited = arvados_cwl.main(
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = [
'arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
'--disable-reuse', "--collection-cache-size=256",
+ "--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
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs('submit_wf_no_reuse.cwl')
def test_submit_container_reuse_disabled_by_workflow(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = [
'arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
- '--disable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--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_no_reuse.cwl', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["use_existing"] = False
- expect_container["name"] = "submit_wf_no_reuse.cwl"
expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
{
"class": "http://arvados.org/cwl#ReuseRequirement",
"enableReuse": False,
},
]
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
"arv": "http://arvados.org/cwl#",
"cwltool": "http://commonwl.org/cwltool#"
}
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
+ "--output-name=Output from workflow submit_wf.cwl",
'--debug', '--on-error=stop',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
"--output-name="+output_name, '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
- '--enable-reuse', "--collection-cache-size=256", "--debug",
+ '--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",
"--storage-classes=foo", '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @mock.patch("arvados_cwl.task_queue.TaskQueue")
+ @stubs
+ def test_submit_multiple_storage_classes(self, stubs):
+ exited = arvados_cwl.main(
+ ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256",
+ "--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']
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+ @mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
- @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
+ @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
@stubs
def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+ final_output_c = arvados.collection.Collection()
+ make_output.return_value = ({},final_output_c)
+
def set_final_output(job_order, output_callback, runtimeContext):
- output_callback("zzzzz-4zz18-zzzzzzzzzzzzzzzz", "success")
+ output_callback({"out": "zzzzz"}, "success")
return []
job.side_effect = set_final_output
exited = arvados_cwl.main(
["--debug", "--local", "--storage-classes=foo",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+ make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
- @mock.patch("arvados_cwl.task_queue.TaskQueue")
+ @mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
- @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection", return_value = (None, None))
+ @mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
@stubs
def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
+ final_output_c = arvados.collection.Collection()
+ make_output.return_value = ({},final_output_c)
+ 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",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', {}, {"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
+ 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({"out": "zzzzz"}, "success")
+ return []
+ job.side_effect = set_final_output
+
+ exited = arvados_cwl.main(
+ ["--debug", "--local",
+ "tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', '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
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
- '--enable-reuse', "--collection-cache-size=256", '--debug',
+ '--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=continue',
"--intermediate-output-ttl=3600",
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
'--debug', '--on-error=continue',
"--trash-intermediate",
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
+ "--output-name=Output 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']
@mock.patch("time.sleep")
@stubs
def test_submit_file_keepref(self, stubs, tm, collectionReader):
+ collectionReader().exists.return_value = True
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
}, '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',
- '--eval-timeout=20', '--thread-count=1',
- '--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 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': {
'vcpus': 1,
'ram': 1342177280
},
- 'use_existing': True,
+ 'use_existing': False,
'properties': {},
'secret_mounts': {}
}
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @mock.patch("arvados.collection.CollectionReader")
- @mock.patch("time.sleep")
- @stubs
- def test_submit_jobs_keepref(self, stubs, tm, reader):
- with open("tests/wf/expect_arvworkflow.cwl") as f:
- reader().open().__enter__().read.return_value = f.read()
-
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug",
- "keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
- del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["y"]
- del expect_pipeline["components"]["cwl-runner"]["script_parameters"]["z"]
- expect_pipeline["components"]["cwl-runner"]["script_parameters"]["cwl:tool"] = "99999999999999999999999999999994+99/expect_arvworkflow.cwl#main"
- expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(exited, 0)
-
@mock.patch("time.sleep")
@stubs
def test_submit_arvworkflow(self, stubs, tm):
],
'requirements': [
{
- 'dockerPull': 'debian:8',
+ 'dockerPull': 'debian:buster-slim',
'class': 'DockerRequirement',
"http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
}
'name': 'a test workflow',
'container_image': "999999999999999999999999999999d3+99",
'command': ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'vcpus': 1,
'ram': 1342177280
},
- 'use_existing': True,
+ 'use_existing': False,
'properties': {
"template_uuid": "962eh-7fd4e-gkbzl62qqtfig37"
},
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs('hello container 123')
def test_submit_container_name(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
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))
@stubs
def test_submit_container_project(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ stubs.api.groups().get().execute.return_value = {"group_class": "project"}
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["owner_uuid"] = project_uuid
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- "--eval-timeout=20", "--thread-count=1",
- '--enable-reuse', "--collection-cache-size=256", '--debug',
+ '--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=continue',
'--project-uuid='+project_uuid,
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=60.0', '--thread-count=1',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=60.0', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=500",
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=20',
'--enable-reuse', "--collection-cache-size=256",
'--debug', '--on-error=continue',
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
- def test_submit_job_runner_image(self, stubs):
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
-
- stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "999999999999999999999999999999d5+99"
-
- expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
- stubs.api.pipeline_instances().create.assert_called_with(
- body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_uuid + '\n')
- self.assertEqual(exited, 0)
-
@stubs
def test_submit_container_runner_image(self, stubs):
exited = arvados_cwl.main(
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs('submit_wf_runner_resources.cwl')
def test_submit_wf_runner_resources(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"vcpus": 2,
"ram": (2000+512) * 2**20
}
- expect_container["name"] = "submit_wf_runner_resources.cwl"
expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
{
"class": "http://arvados.org/cwl#WorkflowRunnerResources",
"keep_cache": 512
}
]
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
"arv": "http://arvados.org/cwl#",
}
expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate',
- '--eval-timeout=20', '--thread-count=1',
- '--enable-reuse', "--collection-cache-size=512", '--debug', '--on-error=continue',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=512",
+ '--output-name=Output from workflow submit_wf_runner_resources.cwl',
+ '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
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")
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},
+ {"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",
"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
"--api=containers",
"--no-log-timestamps",
"--disable-validate",
+ "--disable-color",
"--eval-timeout=20",
- '--thread-count=1',
+ '--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",
"content": {
"$graph": [
{
- "$namespaces": {
- "cwltool": "http://commonwl.org/cwltool#"
- },
"arguments": [
"md5sum",
"example.conf"
"outputs": [
{
"id": "#secret_job.cwl/out",
- "type": "stdout"
+ "type": "File",
+ "outputBinding": {
+ "glob": "hashed_example.txt"
+ }
}
],
"stdout": "hashed_example.txt",
"hints": [
{
"class": "DockerRequirement",
- "dockerPull": "debian:8",
+ "dockerPull": "debian:buster-slim",
"http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
},
{
]
}
],
+ "$namespaces": {
+ "cwltool": "http://commonwl.org/cwltool#"
+ },
"cwlVersion": "v1.0"
},
"kind": "json"
}
},
"name": "secret_wf.cwl",
+ "output_name": "Output from workflow secret_wf.cwl",
"output_path": "/var/spool/cwl",
"priority": 500,
"properties": {},
}
},
"state": "Committed",
- "use_existing": True
+ "use_existing": False
}
stubs.api.container_requests().create.assert_called_with(
@stubs
def test_submit_request_uuid(self, stubs):
+ stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
stubs.api.container_requests().update().execute.return_value = {
self.assertEqual(exited, 1)
@stubs
- def test_submit_uuid_inputs(self, stubs):
+ def test_submit_validate_project_uuid(self, stubs):
+ # Fails with bad cluster prefix
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzb-j7d0g-zzzzzzzzzzzzzzz",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 1)
+
+ # Project lookup fails
+ stubs.api.groups().get().execute.side_effect = Exception("Bad project")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-j7d0g-zzzzzzzzzzzzzzx",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 1)
+
+ # It should work this time because it is looking up a user (and only group is stubbed out to fail)
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid=zzzzz-tpzed-zzzzzzzzzzzzzzx",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+
+
+ @mock.patch("arvados.collection.CollectionReader")
+ @stubs
+ def test_submit_uuid_inputs(self, stubs, collectionReader):
+ collectionReader().exists.return_value = True
+ collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
def list_side_effect(**kwargs):
m = mock.MagicMock()
if "count" in kwargs:
expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['basename'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
- del expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['size']
stubs.api.collections().list.assert_has_calls([
mock.call(count='none',
- filters=[['uuid', 'in', ['zzzzz-4zz18-zzzzzzzzzzzzzzz', 'zzzzz-4zz18-zzzzzzzzzzzzzzz', 'zzzzz-4zz18-zzzzzzzzzzzzzzz']]],
+ filters=[['uuid', 'in', ['zzzzz-4zz18-zzzzzzzzzzzzzzz']]],
select=['uuid', 'portable_data_hash'])])
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
+ @stubs
+ def test_submit_mismatched_uuid_inputs(self, stubs):
+ def list_side_effect(**kwargs):
+ m = mock.MagicMock()
+ if "count" in kwargs:
+ m.execute.return_value = {"items": [
+ {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999997+99"}
+ ]}
+ else:
+ m.execute.return_value = {"items": []}
+ return m
+ stubs.api.collections().list.side_effect = list_side_effect
-class TestCreateTemplate(unittest.TestCase):
- existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
-
- def _adjust_script_params(self, expect_component):
- expect_component['script_parameters']['x'] = {
- 'dataclass': 'File',
- 'required': True,
- 'type': 'File',
- 'value': '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
- }
- expect_component['script_parameters']['y'] = {
- 'dataclass': 'Collection',
- 'required': True,
- 'type': 'Directory',
- 'value': '99999999999999999999999999999998+99',
- }
- expect_component['script_parameters']['z'] = {
- 'dataclass': 'Collection',
- 'required': True,
- 'type': 'Directory',
- }
+ for infile in ("tests/submit_test_job_with_mismatched_uuids.json", "tests/submit_test_job_with_inconsistent_uuids.json"):
+ capture_stderr = StringIO()
+ cwltool_logger = logging.getLogger('cwltool')
+ stderr_logger = logging.StreamHandler(capture_stderr)
+ cwltool_logger.addHandler(stderr_logger)
+
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf.cwl", infile],
+ stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ self.assertEqual(exited, 1)
+ self.assertRegex(
+ re.sub(r'[ \n]+', ' ', capture_stderr.getvalue()),
+ r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99")
+ finally:
+ cwltool_logger.removeHandler(stderr_logger)
+ @mock.patch("arvados.collection.CollectionReader")
@stubs
- def test_create(self, stubs):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
+ collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
+ capture_stderr = StringIO()
+
+ cwltool_logger = logging.getLogger('cwltool')
+ stderr_logger = logging.StreamHandler(capture_stderr)
+ cwltool_logger.addHandler(stderr_logger)
exited = arvados_cwl.main(
- ["--create-workflow", "--debug",
- "--api=jobs",
- "--project-uuid", project_uuid,
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
+ stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ try:
+ self.assertEqual(exited, 1)
+ self.assertRegex(
+ capture_stderr.getvalue(),
+ r"Collection\s*uuid\s*zzzzz-4zz18-zzzzzzzzzzzzzzz\s*not\s*found")
+ finally:
+ cwltool_logger.removeHandler(stderr_logger)
+
+ @stubs('submit_wf_process_properties.cwl')
+ def test_submit_set_process_properties(self, stubs):
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf_process_properties.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- stubs.api.pipeline_instances().create.refute_called()
- stubs.api.jobs().create.refute_called()
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
- expect_component = copy.deepcopy(stubs.expect_job_spec)
- self._adjust_script_params(expect_component)
- expect_template = {
- "components": {
- "submit_wf.cwl": expect_component,
- },
- "name": "submit_wf.cwl",
- "owner_uuid": project_uuid,
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+ {
+ "class": "http://arvados.org/cwl#ProcessProperties",
+ "processProperties": [
+ {"propertyName": "baz",
+ "propertyValue": "$(inputs.x.basename)"},
+ {"propertyName": "foo",
+ "propertyValue": "bar"},
+ {"propertyName": "quux",
+ "propertyValue": {
+ "q1": 1,
+ "q2": 2
+ }
+ }
+ ],
+ }
+ ]
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
+ "arv": "http://arvados.org/cwl#"
}
- stubs.api.pipeline_templates().create.assert_called_with(
- body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+ expect_container["properties"] = {
+ "baz": "blorp.txt",
+ "foo": "bar",
+ "quux": {
+ "q1": 1,
+ "q2": 2
+ }
+ }
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
self.assertEqual(stubs.capture_stdout.getvalue(),
- stubs.expect_pipeline_template_uuid + '\n')
+ stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
- def test_create_name(self, stubs):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ @stubs
+ def test_submit_enable_preemptible(self, stubs):
exited = arvados_cwl.main(
- ["--create-workflow", "--debug",
- "--project-uuid", project_uuid,
- "--api=jobs",
- "--name", "testing 123",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- stubs.api.pipeline_instances().create.refute_called()
- stubs.api.jobs().create.refute_called()
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
+ "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_component = copy.deepcopy(stubs.expect_job_spec)
- self._adjust_script_params(expect_component)
- expect_template = {
- "components": {
- "testing 123": expect_component,
- },
- "name": "testing 123",
- "owner_uuid": project_uuid,
- }
- stubs.api.pipeline_templates().create.assert_called_with(
- body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+ 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',
+ '--enable-preemptible',
+ '/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_pipeline_template_uuid + '\n')
+ stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
@stubs
- def test_update_name(self, stubs):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
-
+ def test_submit_disable_preemptible(self, stubs):
exited = arvados_cwl.main(
- ["--update-workflow", self.existing_template_uuid,
- "--debug",
- "--project-uuid", project_uuid,
- "--api=jobs",
- "--name", "testing 123",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- stubs.capture_stdout, sys.stderr, api_client=stubs.api)
-
- stubs.api.pipeline_instances().create.refute_called()
- stubs.api.jobs().create.refute_called()
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
+ "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_component = copy.deepcopy(stubs.expect_job_spec)
- self._adjust_script_params(expect_component)
- expect_template = {
- "components": {
- "testing 123": expect_component,
- },
- "name": "testing 123",
- "owner_uuid": project_uuid,
- }
- stubs.api.pipeline_templates().create.refute_called()
- stubs.api.pipeline_templates().update.assert_called_with(
- body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
+ 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',
+ '--disable-preemptible',
+ '/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(),
- self.existing_template_uuid + '\n')
+ stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
class TestCreateWorkflow(unittest.TestCase):
existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
expect_workflow = StripYAMLComments(
- open("tests/wf/expect_packed.cwl").read())
+ open("tests/wf/expect_upload_packed.cwl").read().rstrip())
+
+ def setUp(self):
+ cwltool.process._names = set()
+ arvados_cwl.arvdocker.arv_docker_clear_cache()
+
+ 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"}
exited = arvados_cwl.main(
["--create-workflow", "--debug",
@stubs
def test_create_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ stubs.api.groups().get().execute.return_value = {"group_class": "project"}
exited = arvados_cwl.main(
["--create-workflow", "--debug",
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
- def test_incompatible_api(self, stubs):
- capture_stderr = io.StringIO()
- acr_logger = logging.getLogger('arvados.cwl-runner')
- stderr_logger = logging.StreamHandler(capture_stderr)
- acr_logger.addHandler(stderr_logger)
-
- exited = arvados_cwl.main(
- ["--update-workflow", self.existing_workflow_uuid,
- "--api=jobs",
- "--debug",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stderr, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 1)
- self.assertRegexpMatches(
- capture_stderr.getvalue(),
- "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
- acr_logger.removeHandler(stderr_logger)
@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",
"name": "submit_wf.cwl",
"description": "",
"definition": self.expect_workflow,
+ "owner_uuid": project_uuid
}
}
stubs.api.workflows().update.assert_called_with(
self.existing_workflow_uuid + '\n')
self.assertEqual(exited, 0)
+
@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",
"name": "testing 123",
"description": "",
"definition": self.expect_workflow,
+ "owner_uuid": project_uuid
}
}
stubs.api.workflows().update.assert_called_with(
@stubs
def test_create_collection_per_tool(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ stubs.api.groups().get().execute.return_value = {"group_class": "project"}
exited = arvados_cwl.main(
["--create-workflow", "--debug",
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
- expect_workflow = StripYAMLComments(open(toolfile).read())
+ expect_workflow = StripYAMLComments(open(toolfile).read().rstrip())
body = {
"workflow": {
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
-class TestTemplateInputs(unittest.TestCase):
- expect_template = {
- "components": {
- "inputs_test.cwl": {
- 'runtime_constraints': {
- 'docker_image': '999999999999999999999999999999d3+99',
- 'min_ram_mb_per_node': 1024
- },
- 'script_parameters': {
- 'cwl:tool':
- 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main',
- 'optionalFloatInput': None,
- 'fileInput': {
- 'type': 'File',
- 'dataclass': 'File',
- 'required': True,
- 'title': "It's a file; we expect to find some characters in it.",
- 'description': 'If there were anything further to say, it would be said here,\nor here.'
- },
- 'floatInput': {
- 'type': 'float',
- 'dataclass': 'number',
- 'required': True,
- 'title': 'Floats like a duck',
- 'default': 0.1,
- 'value': 0.1,
- },
- 'optionalFloatInput': {
- 'type': ['null', 'float'],
- 'dataclass': 'number',
- 'required': False,
- },
- 'boolInput': {
- 'type': 'boolean',
- 'dataclass': 'boolean',
- 'required': True,
- 'title': 'True or false?',
- },
- },
- 'repository': 'arvados',
- 'script_version': 'master',
- 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
- 'script': 'cwl-runner',
- },
- },
- "name": "inputs_test.cwl",
- }
-
@stubs
- def test_inputs_empty(self, stubs):
+ def test_create_with_imports(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ stubs.api.groups().get().execute.return_value = {"group_class": "project"}
+
exited = arvados_cwl.main(
- ["--create-template",
- "tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
+ ["--create-workflow", "--debug",
+ "--api=containers",
+ "--project-uuid", project_uuid,
+ "tests/wf/feddemo/feddemo.cwl"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
- stubs.api.pipeline_templates().create.assert_called_with(
- body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
+ stubs.api.pipeline_templates().create.refute_called()
+ stubs.api.container_requests().create.refute_called()
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
@stubs
- def test_inputs(self, stubs):
+ def test_create_with_no_input(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ stubs.api.groups().get().execute.return_value = {"group_class": "project"}
+
exited = arvados_cwl.main(
- ["--create-template",
- "tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
+ ["--create-workflow", "--debug",
+ "--api=containers",
+ "--project-uuid", project_uuid,
+ "tests/wf/revsort/revsort.cwl"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
- expect_template = copy.deepcopy(self.expect_template)
- params = expect_template[
- "components"]["inputs_test.cwl"]["script_parameters"]
- params["fileInput"]["value"] = '169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'
- params["cwl:tool"] = 'a2de777156fb700f1363b1f2e370adca+60/workflow.cwl#main'
- params["floatInput"]["value"] = 1.234
- params["boolInput"]["value"] = True
+ stubs.api.pipeline_templates().create.refute_called()
+ stubs.api.container_requests().create.refute_called()
- stubs.api.pipeline_templates().create.assert_called_with(
- body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
projects / arvados.git / blobdiff