"project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
})
- def make_tool(toolpath_object, loadingContext):
- return arvados_cwl.ArvadosCommandTool(runner, toolpath_object, loadingContext)
- runner.arv_make_tool.side_effect = make_tool
+ 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
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool"
+ "id": "",
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2"
})
loadingContext, runtimeContext = self.helper(runner, enable_reuse)
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
'name': 'test_run_'+str(enable_reuse),
'runtime_constraints': {
'vcpus': 1,
- 'ram': 1073741824
+ 'ram': 268435456
},
'use_existing': enable_reuse,
'priority': 500,
# For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
@mock.patch("arvados.commands.keepdocker.list_images_in_arv")
def test_resource_requirements(self, keepdocker):
+ arvados_cwl.add_arv_hints()
runner = mock.MagicMock()
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 3600
"class": "http://arvados.org/cwl#IntermediateOutput",
"outputTTL": 7200
}, {
- "class": "http://arvados.org/cwl#ReuseRequirement",
+ "class": "WorkReuse",
"enableReuse": False
}],
"baseCommand": "ls",
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool"
+ "id": "",
+ "class": "CommandLineTool",
+ "cwlVersion": "v1.2"
})
loadingContext, runtimeContext = self.helper(runner)
runtimeContext.name = "test_resource_requirements"
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
"stderr": "stderr.txt",
"stdin": "/keep/99999999999999999999999999999996+99/file.txt",
"arguments": [{"valueFrom": "$(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,
# 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.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": "nvidia-smi",
+ "baseCommand": "echo",
"arguments": [],
- "id": "#",
- "class": "org.w3id.cwl.cwl.CommandLineTool",
- "hints": [
- {
- "class": "http://arvados.org/cwl#CUDARequirement",
- "minCUDADriverVersion": "11.0",
- "minCUDAHardwareCapability": "9.0",
- }
- ]
+ "id": "",
+ "cwlVersion": "v1.2",
+ "class": "CommandLineTool"
})
loadingContext, runtimeContext = self.helper(runner, True)
- arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+ arvtool = cwltool.load_tool.load_tool(tool, loadingContext)
arvtool.formatgraph = None
+ container_request = {
+ 'environment': {
+ 'HOME': '/var/spool/cwl',
+ 'TMPDIR': '/tmp'
+ },
+ 'name': 'test_run_True',
+ '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 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({
- 'environment': {
- 'HOME': '/var/spool/cwl',
- 'TMPDIR': '/tmp'
- },
- 'name': 'test_run_True',
- 'runtime_constraints': {
- 'vcpus': 1,
- 'ram': 1073741824,
- 'cuda': {
- 'device_count': 1,
- 'driver_version': "11.0",
- 'hardware_capability': "9.0"
- }
- },
- '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': '99999999999999999999999999999993+99',
- 'command': ['nvidia-smi'],
- 'cwd': '/var/spool/cwl',
- 'scheduling_parameters': {},
- 'properties': {},
- 'secret_mounts': {},
- 'output_storage_classes': ["default"]
- }))
+ 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))
+
class TestWorkflow(unittest.TestCase):
projects / arvados.git / blobdiff