13219: Adds TimeLimit support on arvados-cwl-runner

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 667f9262f7f92f3c70c59fdad32a0c2a1412ca6a..4ebcefb1365029a9f70665cbddedc71ffa8172bc 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -239,6 +239,9 @@ class ArvadosContainer(JobBase):
         if self.output_ttl < 0:
             raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
 
+        if self.timelimit is not None:
+            scheduling_parameters["max_run_time"] = self.timelimit
+
         container_request["output_ttl"] = self.output_ttl
         container_request["mounts"] = mounts
         container_request["secret_mounts"] = secret_mounts

diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index af6f7721fe82eb3ec0ffa943a0f191391aac75e2..dad6313771f0a23fab759b970112e3ab0de9d09b 100644 (file)
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -648,3 +648,76 @@ class TestContainer(unittest.TestCase):
                         }
                     }
                 }))
+
+    # 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_timelimit(self, keepdocker):
+        arv_docker_clear_cache()
+
+        runner = mock.MagicMock()
+        runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+        runner.ignore_docker_for_reuse = False
+        runner.intermediate_output_ttl = 0
+        runner.secret_store = cwltool.secrets.SecretStore()
+
+        keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
+        runner.api.collections().get().execute.return_value = {
+            "portable_data_hash": "99999999999999999999999999999993+99"}
+
+        tool = cmap({
+            "inputs": [],
+            "outputs": [],
+            "baseCommand": "ls",
+            "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+            "id": "#",
+            "class": "CommandLineTool",
+            "hints": [
+                {
+                    "class": "http://commonwl.org/cwltool#TimeLimit",
+                    "timelimit": 42
+                }
+            ]
+        })
+
+        loadingContext, runtimeContext = self.helper(runner)
+        runtimeContext.name = "test_timelimit"
+
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, 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_timelimit',
+                    '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',
+                    'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+                    'output_path': '/var/spool/cwl',
+                    'output_ttl': 0,
+                    'container_image': 'arvados/jobs',
+                    'command': ['ls', '/var/spool/cwl'],
+                    'cwd': '/var/spool/cwl',
+                    'scheduling_parameters': {
+                        "max_run_time": 42
+                    },
+                    'properties': {},
+                    'secret_mounts': {}
+                }))