14018: Setting process properties WIP

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml b/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml
index 17c37cf5c97414dbfc7b6bf692c51861dcf67fe0..09951a9848de5a765128a32714bc79ed52ed3638 100644 (file)
--- a/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml
+++ b/sdk/cwl/arvados_cwl/arv-cwl-schema-v1.2.yml
@@ -251,7 +251,7 @@ $graph:
       type: string
       doc: The property key
     - name: propertyValue
-      type: [cwl:Expression, Any]
+      type: [Any]
       doc: The property value
 
 
@@ -271,6 +271,6 @@ $graph:
         _type: "@vocab"
     processProperties:
       type: PropertyDef[]
-      jsonldPredicate:
-        mapSubject: propertyName
-        mapPredicate: propertyValue
+      #jsonldPredicate:
+      #  mapSubject: propertyName
+      #  mapPredicate: propertyValue

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index c6e4577d03bcd8d36af869d8b6ec63cc2531bc47..3065e1a7cd18cd431aff04e72e97477e08ace088 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -28,7 +28,7 @@ import arvados.collection
 
 from .arvdocker import arv_docker_get_image
 from . import done
-from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields
+from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields, make_builder
 from .fsaccess import CollectionFetcher
 from .pathmapper import NoFollowPathMapper, trim_listing
 from .perf import Perf
@@ -482,8 +482,10 @@ class RunnerContainer(Runner):
         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
         if properties_req:
             builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
+            print("ZZZZZZ", properties_req["processProperties"])
             for pr in properties_req["processProperties"]:
-                container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
+                print("ZZZZZZ", pr)
+                container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
 
         # --local means execute the workflow instead of submitting a container request
         # --api=containers means use the containers API

diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index 2b46b89c604cafc0f91ee3966ecd1a3c068dbad7..91283b0b622c5719630c82c19bb3c2c46ac7133f 100644 (file)
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -914,6 +914,97 @@ 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_setting_process_properties(self, keepdocker):
+        arv_docker_clear_cache()
+
+        runner = mock.MagicMock()
+        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": [
+                {"id": "x", "type": "string"}],
+            "outputs": [],
+            "baseCommand": "ls",
+            "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+            "id": "#",
+            "class": "CommandLineTool",
+            "hints": [
+            {
+                "class": "http://arvados.org/cwl#ProcessProperties",
+                "processProperties": [
+                    {"propertyName": "foo",
+                     "propertyValue": "bar"},
+                    {"propertyName": "baz",
+                     "propertyValue": "$(inputs.x)"},
+                    {"propertyName": "quux",
+                     "propertyValue": {
+                         "q1": 1,
+                         "q2": 2
+                     }
+                    }
+                ],
+            }
+        ]
+        })
+
+        loadingContext, runtimeContext = self.helper(runner, True)
+
+        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
+        arvtool.formatgraph = None
+
+        for j in arvtool.job({"x": "blorp"}, 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
+                    },
+                    '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': ['ls', '/var/spool/cwl'],
+                    'cwd': '/var/spool/cwl',
+                    'scheduling_parameters': {},
+                    'properties': {
+                        "baz": "blorp",
+                        "foo": "bar",
+                        "quux": {
+                            "q1": 1,
+                            "q2": 2
+                        }
+                    },
+                    'secret_mounts': {},
+                    'output_storage_classes': ["default"]
+                }))
+
+
 class TestWorkflow(unittest.TestCase):
     def setUp(self):
         cwltool.process._names = set()

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 1b646a8e4459dfe5677fb18ca997a393248b6e8f..2889ce331e4936d95f3b2de34c52bd0acd93e07b 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -1419,6 +1419,51 @@ class TestSubmit(unittest.TestCase):
         finally:
             cwltool_logger.removeHandler(stderr_logger)
 
+    @stubs
+    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)
+
+        expect_container = copy.deepcopy(stubs.expect_container_spec)
+        expect_container["name"] = "submit_wf_process_properties.cwl"
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+            {
+                "class": "http://arvados.org/cwl#ProcessProperties",
+                "processProperties": [
+                    {"propertyName": "foo",
+                     "propertyValue": "bar"},
+                    {"propertyName": "baz",
+                     "propertyValue": "$(inputs.x.basename)"},
+                    {"propertyName": "quux",
+                     "propertyValue": {
+                         "q1": 1,
+                         "q2": 2
+                     }
+                    }
+                ],
+            }
+        ]
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+            "arv": "http://arvados.org/cwl#"
+        }
+
+        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_container_request_uuid + '\n')
+        self.assertEqual(exited, 0)
+
 
 class TestCreateWorkflow(unittest.TestCase):
     existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"