import unittest
import os
import functools
+import threading
import cwltool.process
import cwltool.secrets
+import cwltool.load_tool
from cwltool.update import INTERNAL_VERSION
from schema_salad.ref_resolver import Loader
from schema_salad.sourceline import cmap
cwltool.process._names = set()
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
+
def helper(self, runner, enable_reuse=True):
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(INTERNAL_VERSION)
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
+ fs_access = mock.MagicMock()
+ fs_access.exists.return_value = True
+
loadingContext = arvados_cwl.context.ArvLoadingContext(
{"avsc_names": avsc_names,
"basedir": "",
"make_fs_access": make_fs_access,
+ "construct_tool_object": runner.arv_make_tool,
+ "fetcher_constructor": functools.partial(arvados_cwl.CollectionFetcher, api_client=runner.api, fs_access=fs_access),
"loader": Loader({}),
- "metadata": {"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}})
+ "metadata": cmap({"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"})
+ })
runtimeContext = arvados_cwl.context.ArvRuntimeContext(
{"work_api": "containers",
"basedir": "",
"name": "test_run_"+str(enable_reuse),
"make_fs_access": make_fs_access,
"tmpdir": "/tmp",
+ "outdir": "/tmp",
"enable_reuse": enable_reuse,
"priority": 500,
- "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
+ "workflow_eval_lock": threading.Condition(threading.RLock())
})
+ if isinstance(runner, mock.MagicMock):
+ def make_tool(toolpath_object, loadingContext):
+ return arvados_cwl.ArvadosCommandTool(runner, toolpath_object, loadingContext)
+ runner.arv_make_tool.side_effect = make_tool
+
return loadingContext, runtimeContext
# Helper function to set up the ArvCwlExecutor to use the containers api
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool"
+ "id": "",
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2"
})
loadingContext, runtimeContext = self.helper(runner, enable_reuse)
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
'name': 'test_run_'+str(enable_reuse),
'runtime_constraints': {
'vcpus': 1,
- 'ram': 1073741824
+ 'ram': 268435456
},
'use_existing': enable_reuse,
'priority': 500,
# For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
def test_resource_requirements(self, keepdocker):
+ arvados_cwl.add_arv_hints()
runner = mock.MagicMock()
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 3600
"class": "http://arvados.org/cwl#IntermediateOutput",
"outputTTL": 7200
}, {
- "class": "http://arvados.org/cwl#ReuseRequirement",
+ "class": "WorkReuse",
"enableReuse": False
}],
"baseCommand": "ls",
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool"
+ "id": "",
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_resource_requirements"
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
} ]
}],
"baseCommand": "ls",
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool"
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2",
+ "id": ""
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_initial_work_dir"
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
+
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
'name': 'test_initial_work_dir',
'runtime_constraints': {
'vcpus': 1,
- 'ram': 1073741824
+ 'ram': 268435456
},
'use_existing': True,
'priority': 500,
"stderr": "stderr.txt",
"stdin": "/keep/99999999999999999999999999999996+99/file.txt",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool"
+ "id": "",
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_run_redirect"
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
'name': 'test_run_redirect',
'runtime_constraints': {
'vcpus': 1,
- 'ram': 1073741824
+ 'ram': 268435456
},
'use_existing': True,
'priority': 500,
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool"
+ "id": "",
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_run_mounts"
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
job_order = {
"p1": {
'name': 'test_run_mounts',
'runtime_constraints': {
'vcpus': 1,
- 'ram': 1073741824
+ 'ram': 268435456
},
'use_existing': True,
'priority': 500,
# Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
def test_secrets(self, keepdocker):
+ arvados_cwl.add_arv_hints()
runner = mock.MagicMock()
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 0
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
tool = cmap({"arguments": ["md5sum", "example.conf"],
- "class": "org.w3id.cwl.cwl.CommandLineTool",
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2",
"hints": [
{
"class": "http://commonwl.org/cwltool#Secrets",
]
}
],
- "id": "#secret_job.cwl",
+ "id": "",
"inputs": [
{
"id": "#secret_job.cwl/pw",
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_secrets"
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
job_order = {"pw": "blorp"}
'name': 'test_secrets',
'runtime_constraints': {
'vcpus': 1,
- 'ram': 1073741824
+ 'ram': 268435456
},
'use_existing': True,
'priority': 500,
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool",
+ "id": "",
+ "cwlVersion": "v1.2",
+ "class": "CommandLineTool",
"hints": [
{
"class": "ToolTimeLimit",
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_timelimit"
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool",
+ "id": "",
+ "cwlVersion": "v1.2",
+ "class": "CommandLineTool",
"hints": [
{
"class": "http://arvados.org/cwl#OutputStorageClass",
loadingContext, runtimeContext = self.helper(runner, True)
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
'name': 'test_run_True',
'runtime_constraints': {
'vcpus': 1,
- 'ram': 1073741824
+ 'ram': 268435456
},
'use_existing': True,
'priority': 500,
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool",
+ "id": "",
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2",
"hints": [
{
"class": "http://arvados.org/cwl#ProcessProperties",
loadingContext, runtimeContext = self.helper(runner, True)
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({"x": "blorp"}, mock.MagicMock(), runtimeContext):
'name': 'test_run_True',
'runtime_constraints': {
'vcpus': 1,
- 'ram': 1073741824
+ 'ram': 268435456
},
'use_existing': True,
'priority': 500,
}))
+ # The test passes no builder.resources
+ # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
+ def test_cuda_requirement(self, keepdocker):
+ arvados_cwl.add_arv_hints()
+ arv_docker_clear_cache()
+
+ runner = mock.MagicMock()
+ runner.ignore_docker_for_reuse = False
+ runner.intermediate_output_ttl = 0
+ runner.secret_store = cwltool.secrets.SecretStore()
+ runner.api._rootDesc = {"revision": "20210628"}
+
+ keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
+ runner.api.collections().get().execute.return_value = {
+ "portable_data_hash": "99999999999999999999999999999993+99"}
+
+ test_cwl_req = [{
+ "class": "http://commonwl.org/cwltool#CUDARequirement",
+ "cudaVersionMin": "11.0",
+ "cudaComputeCapability": "9.0",
+ }, {
+ "class": "http://commonwl.org/cwltool#CUDARequirement",
+ "cudaVersionMin": "11.0",
+ "cudaComputeCapability": "9.0",
+ "cudaDeviceCountMin": 2
+ }, {
+ "class": "http://commonwl.org/cwltool#CUDARequirement",
+ "cudaVersionMin": "11.0",
+ "cudaComputeCapability": ["4.0", "5.0"],
+ "cudaDeviceCountMin": 2
+ }]
+
+ test_arv_req = [{
+ 'device_count': 1,
+ 'driver_version': "11.0",
+ 'hardware_capability': "9.0"
+ }, {
+ 'device_count': 2,
+ 'driver_version': "11.0",
+ 'hardware_capability': "9.0"
+ }, {
+ 'device_count': 2,
+ 'driver_version': "11.0",
+ 'hardware_capability': "4.0"
+ }]
+
+ for test_case in range(0, len(test_cwl_req)):
+
+ tool = cmap({
+ "inputs": [],
+ "outputs": [],
+ "baseCommand": "nvidia-smi",
+ "arguments": [],
+ "id": "",
+ "cwlVersion": "v1.2",
+ "class": "CommandLineTool",
+ "requirements": [test_cwl_req[test_case]]
+ })
+
+ loadingContext, runtimeContext = self.helper(runner, True)
+
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
+ arvtool.formatgraph = None
+
+ for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
+ j.run(runtimeContext)
+ runner.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'environment': {
+ 'HOME': '/var/spool/cwl',
+ 'TMPDIR': '/tmp'
+ },
+ 'name': 'test_run_True' + ("" if test_case == 0 else "_"+str(test_case+1)),
+ 'runtime_constraints': {
+ 'vcpus': 1,
+ 'ram': 268435456,
+ 'cuda': test_arv_req[test_case]
+ },
+ 'use_existing': True,
+ 'priority': 500,
+ 'mounts': {
+ '/tmp': {'kind': 'tmp',
+ "capacity": 1073741824
+ },
+ '/var/spool/cwl': {'kind': 'tmp',
+ "capacity": 1073741824 }
+ },
+ 'state': 'Committed',
+ 'output_name': 'Output for step test_run_True' + ("" if test_case == 0 else "_"+str(test_case+1)),
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'output_path': '/var/spool/cwl',
+ 'output_ttl': 0,
+ 'container_image': '99999999999999999999999999999993+99',
+ 'command': ['nvidia-smi'],
+ 'cwd': '/var/spool/cwl',
+ 'scheduling_parameters': {},
+ 'properties': {},
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
+ }))
+
+
+ # The test passes no builder.resources
+ # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ @mock.patch("arvados_cwl.arvdocker.determine_image_id")
+ @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
+ def test_match_local_docker(self, keepdocker, determine_image_id):
+ arvados_cwl.add_arv_hints()
+ arv_docker_clear_cache()
+
+ runner = mock.MagicMock()
+ runner.ignore_docker_for_reuse = False
+ runner.intermediate_output_ttl = 0
+ runner.secret_store = cwltool.secrets.SecretStore()
+ runner.api._rootDesc = {"revision": "20210628"}
+
+ keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz4", {"dockerhash": "456"}),
+ ("zzzzz-4zz18-zzzzzzzzzzzzzz3", {"dockerhash": "123"})]
+ determine_image_id.side_effect = lambda x: "123"
+ def execute(uuid):
+ ex = mock.MagicMock()
+ lookup = {"zzzzz-4zz18-zzzzzzzzzzzzzz4": {"portable_data_hash": "99999999999999999999999999999994+99"},
+ "zzzzz-4zz18-zzzzzzzzzzzzzz3": {"portable_data_hash": "99999999999999999999999999999993+99"}}
+ ex.execute.return_value = lookup[uuid]
+ return ex
+ runner.api.collections().get.side_effect = execute
+
+ tool = cmap({
+ "inputs": [],
+ "outputs": [],
+ "baseCommand": "echo",
+ "arguments": [],
+ "id": "",
+ "cwlVersion": "v1.0",
+ "class": "org.w3id.cwl.cwl.CommandLineTool"
+ })
+
+ loadingContext, runtimeContext = self.helper(runner, True)
+
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool.formatgraph = None
+
+ container_request = {
+ 'environment': {
+ 'HOME': '/var/spool/cwl',
+ 'TMPDIR': '/tmp'
+ },
+ 'name': 'test_run_True',
+ 'runtime_constraints': {
+ 'vcpus': 1,
+ 'ram': 1073741824,
+ },
+ 'use_existing': True,
+ 'priority': 500,
+ 'mounts': {
+ '/tmp': {'kind': 'tmp',
+ "capacity": 1073741824
+ },
+ '/var/spool/cwl': {'kind': 'tmp',
+ "capacity": 1073741824 }
+ },
+ 'state': 'Committed',
+ 'output_name': 'Output for step test_run_True',
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'output_path': '/var/spool/cwl',
+ 'output_ttl': 0,
+ 'container_image': '99999999999999999999999999999994+99',
+ 'command': ['echo'],
+ 'cwd': '/var/spool/cwl',
+ 'scheduling_parameters': {},
+ 'properties': {},
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
+ }
+
+ runtimeContext.match_local_docker = False
+ for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
+ j.run(runtimeContext)
+ runner.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(container_request))
+
+ arv_docker_clear_cache()
+ runtimeContext.match_local_docker = True
+ container_request['container_image'] = '99999999999999999999999999999993+99'
+ container_request['name'] = 'test_run_True_2'
+ container_request['output_name'] = 'Output for step test_run_True_2'
+ for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
+ j.run(runtimeContext)
+ runner.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(container_request))
+
+
+ # The test passes no builder.resources
+ # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
+ def test_run_preemptible_hint(self, keepdocker):
+ arvados_cwl.add_arv_hints()
+ for enable_preemptible in (None, True, False):
+ for preemptible_hint in (None, True, False):
+ arv_docker_clear_cache()
+
+ runner = mock.MagicMock()
+ runner.ignore_docker_for_reuse = False
+ runner.intermediate_output_ttl = 0
+ runner.secret_store = cwltool.secrets.SecretStore()
+ runner.api._rootDesc = {"revision": "20210628"}
+
+ keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
+ runner.api.collections().get().execute.return_value = {
+ "portable_data_hash": "99999999999999999999999999999993+99"}
+
+ if preemptible_hint is not None:
+ hints = [{
+ "class": "http://arvados.org/cwl#UsePreemptible",
+ "usePreemptible": preemptible_hint
+ }]
+ else:
+ hints = []
+
+ tool = cmap({
+ "inputs": [],
+ "outputs": [],
+ "baseCommand": "ls",
+ "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+ "id": "",
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2",
+ "hints": hints
+ })
+
+ loadingContext, runtimeContext = self.helper(runner)
+
+ runtimeContext.name = 'test_run_enable_preemptible_'+str(enable_preemptible)+str(preemptible_hint)
+ runtimeContext.enable_preemptible = enable_preemptible
+
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
+ arvtool.formatgraph = None
+
+ # Test the interactions between --enable/disable-preemptible
+ # and UsePreemptible hint
+
+ if enable_preemptible is None:
+ if preemptible_hint is None:
+ sched = {}
+ else:
+ sched = {'preemptible': preemptible_hint}
+ else:
+ if preemptible_hint is None:
+ sched = {'preemptible': enable_preemptible}
+ else:
+ sched = {'preemptible': enable_preemptible and preemptible_hint}
+
+ for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
+ j.run(runtimeContext)
+ runner.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'environment': {
+ 'HOME': '/var/spool/cwl',
+ 'TMPDIR': '/tmp'
+ },
+ 'name': runtimeContext.name,
+ 'runtime_constraints': {
+ 'vcpus': 1,
+ 'ram': 268435456
+ },
+ 'use_existing': True,
+ 'priority': 500,
+ 'mounts': {
+ '/tmp': {'kind': 'tmp',
+ "capacity": 1073741824
+ },
+ '/var/spool/cwl': {'kind': 'tmp',
+ "capacity": 1073741824 }
+ },
+ 'state': 'Committed',
+ 'output_name': 'Output for step '+runtimeContext.name,
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'output_path': '/var/spool/cwl',
+ 'output_ttl': 0,
+ 'container_image': '99999999999999999999999999999993+99',
+ 'command': ['ls', '/var/spool/cwl'],
+ 'cwd': '/var/spool/cwl',
+ 'scheduling_parameters': sched,
+ 'properties': {},
+ 'secret_mounts': {},
+ 'output_storage_classes': ["default"]
+ }))
+
+
+
class TestWorkflow(unittest.TestCase):
def setUp(self):
cwltool.process._names = set()
runner.api.collections().list().execute.return_value = {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz",
"portable_data_hash": "99999999999999999999999999999993+99"}]}
+ runner.api.containers().current().execute.return_value = {}
+
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
projects / arvados.git / blobdiff