Added default engine logic and tests

dnastack/cli/workbench/runs_commands.py

@@ -7,7 +7,7 @@
 
 from dnastack.cli.workbench.utils import get_ewes_client
 from dnastack.client.workbench.ewes.models import ExtendedRunListOptions, ExtendedRunRequest, BatchRunRequest, \
-    MinimalExtendedRunWithOutputs, MinimalExtendedRunWithInputs, TaskListOptions, State
+    MinimalExtendedRunWithOutputs, MinimalExtendedRunWithInputs, TaskListOptions, State, ExecutionEngineListOptions
 from dnastack.client.workbench.ewes.models import LogType
 from dnastack.cli.helpers.command.decorator import command
 from dnastack.cli.helpers.command.spec import ArgumentSpec
@@ -438,8 +438,9 @@ def write_logs(iterable: Iterable[bytes], writer):
                  name='default_workflow_engine_parameters',
                  arg_names=['--engine-params'],
                  help='Set the global engine parameters for all runs that are to be submitted. '
-                      'Engine params can be specified as a KV pair, inlined JSON, or as a json file preceded by the "@"'
-                      'symbol.',
+                      'Engine params can be specified as inlined JSON, json file preceded by the "@" symbol, '
+                      'KV pair, parameter preset ID, or as a list of KV pairs and preset IDs separated by commas '
+                      '(e.g. my-preset-id,key=value).',
                  as_option=True,
                  default=None,
                  required=False
@@ -478,8 +479,8 @@ def write_logs(iterable: Iterable[bytes], writer):
              ),
              ArgumentSpec(
                  name='overrides',
-                 help='Additional arguments to set input values for all runs. The override values can be any JSON-like value'
-                      'such as inline JSON, command separated key value pairs or'
+                 help='Additional arguments to set input values for all runs. The override values can be any '
+                      'JSON-like value such as inline JSON, command separated key value pairs or '
                       'a json file referenced preceded by the "@" symbol.',
                  as_option=False,
                  default=None,
@@ -506,24 +507,36 @@ def submit_batch(context: Optional[str],
 
     ewes_client = get_ewes_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
 
+    def get_default_engine_id():
+        list_options = ExecutionEngineListOptions()
+        engines = ewes_client.list_engines(list_options)
+        for engine in engines:
+            if engine.default:
+                return engine.id
+        raise ValueError("No default engine found. Please specify an engine id in "
+                         "the workflow engine parameters list using ENGINE_ID_KEY=....")
+
     if default_workflow_engine_parameters:
         possible_literal_or_file = default_workflow_engine_parameters.return_parsed_literal_or_file()
         if possible_literal_or_file:
             default_workflow_engine_parameters = possible_literal_or_file
         else:
             [param_ids_list, kv_pairs_list] = default_workflow_engine_parameters.separate_strings_and_kvps()
             param_presets = dict()
-            for param_id in param_ids_list:
-                try:
-                    param_preset = ewes_client.get_engine_param_preset(engine_id, param_id)
-                    param_presets.update(param_preset.preset_values)
-                except Exception as e:
-                    raise ValueError(f"Unable to find engine parameter preset with id {param_id}. "
-                                     f"You may only specify parameter preset ids and key value pairs in a list "
-                                     f"together. To include file content or JSON literals, it must be specified "
-                                     f"as a key-value pair. For more information please refer to "
-                                     f"https://docs.omics.ai/products/command-line-interface/"
-                                     f"working-with-json-data. {e}")
+            if param_ids_list:
+                if not engine_id:
+                    engine_id = get_default_engine_id()
+                for param_id in param_ids_list:
+                    try:
+                        param_preset = ewes_client.get_engine_param_preset(engine_id, param_id)
+                        param_presets.update(param_preset.preset_values)
+                    except Exception as e:
+                        raise ValueError(f"Unable to find engine parameter preset with id {param_id}. "
+                                         f"You may only specify parameter preset ids and key value pairs in a list "
+                                         f"together. To include file content or JSON literals, it must be specified "
+                                         f"as a key-value pair. For more information please refer to "
+                                         f"https://docs.omics.ai/products/command-line-interface/"
+                                         f"working-with-json-data. {e}")
 
             if kv_pairs_list:  # if there are key value pairs left
                 try:

tests/cli/test_workbench.py

@@ -10,7 +10,8 @@
 
 from dnastack.alpha.client.workflow.models import Workflow, WorkflowVersion
 from dnastack.client.workbench.ewes.models import ExtendedRunStatus, ExtendedRun, BatchActionResult, BatchRunResponse, \
-    MinimalExtendedRunWithInputs, MinimalExtendedRun, MinimalExtendedRunWithOutputs, ExecutionEngine, EngineParamPreset
+    MinimalExtendedRunWithInputs, MinimalExtendedRun, MinimalExtendedRunWithOutputs, ExecutionEngine, EngineParamPreset, \
+    BatchRunRequest
 from .base import WorkbenchCliTestCase
 
 
@@ -353,6 +354,70 @@ def test_submit_batch_with_multiple_params():
 
         test_submit_batch_with_multiple_params()
 
+        def test_submit_batch_with_engine_key_value_param():
+            submitted_batch = BatchRunResponse(**self.simple_invoke(
+                'workbench', 'runs', 'submit',
+                '--url', hello_world_workflow_url,
+                '--engine-params', 'key=value'
+            ))
+            self.assertEqual(len(submitted_batch.runs), 1, 'Expected exactly one run to be submitted.')
+            described_runs = [ExtendedRun(**described_run) for described_run in self.simple_invoke(
+                'workbench', 'runs', 'describe',
+                submitted_batch.runs[0].run_id
+            )]
+            self.assertEqual(len(described_runs), 1, f'Expected exactly one run. Found {described_runs}')
+            self.assertEqual(described_runs[0].request.workflow_engine_parameters, {'key': 'value'},
+                             f'Expected workflow engine params to be exactly the same. '
+                             f'Found {described_runs[0].request.workflow_engine_parameters}')
+
+        test_submit_batch_with_engine_key_value_param()
+
+        def test_submit_batch_with_engine_preset_param():
+            submitted_batch = BatchRunResponse(**self.simple_invoke(
+                'workbench', 'runs', 'submit',
+                '--url', hello_world_workflow_url,
+                '--engine-params', self.engine_params.id,
+            ))
+            self.assertEqual(len(submitted_batch.runs), 1, 'Expected exactly one run to be submitted.')
+            described_runs = [ExtendedRun(**described_run) for described_run in self.simple_invoke(
+                'workbench', 'runs', 'describe',
+                submitted_batch.runs[0].run_id
+            )]
+
+            self.assertEqual(len(described_runs), 1, f'Expected exactly one run. Found {described_runs}')
+            processed_engine_params = {'engine_id': self.execution_engine.id}
+            processed_engine_params.update(self.engine_params.preset_values)
+            self.assertEqual(described_runs[0].request.workflow_engine_parameters, processed_engine_params,
+                             f'Expected workflow engine params to be exactly the same. '
+                             f'Found {described_runs[0].request.workflow_engine_parameters}')
+
+        test_submit_batch_with_engine_preset_param()
+
+        def test_submit_batch_with_mixed_engine_preset_param_types():
+            submitted_batch = BatchRunResponse(**self.simple_invoke(
+                'workbench', 'runs', 'submit',
+                '--url', hello_world_workflow_url,
+                '--engine-params', f'goodbye=moon,{self.engine_params.id},hello=world',
+            ))
+            self.assertEqual(len(submitted_batch.runs), 1, 'Expected exactly one run to be submitted.')
+            described_runs = [ExtendedRun(**described_run) for described_run in self.simple_invoke(
+                'workbench', 'runs', 'describe',
+                submitted_batch.runs[0].run_id
+            )]
+
+            self.assertEqual(len(described_runs), 1, f'Expected exactly one run. Found {described_runs}')
+            processed_engine_params = {
+                'engine_id': self.execution_engine.id,
+                'goodbye': 'moon',
+                'hello': 'world',
+                **self.engine_params.preset_values
+            }
+            self.assertEqual(described_runs[0].request.workflow_engine_parameters, processed_engine_params,
+                             f'Expected workflow engine params to be exactly the same. '
+                             f'Found {described_runs[0].request.workflow_engine_parameters}')
+
+        test_submit_batch_with_mixed_engine_preset_param_types()
+
     def test_workflows_list(self):
         result = [Workflow(**workflow) for workflow in self.simple_invoke(
             'workbench', 'workflows', 'list'

tests/exam_helper_for_workbench.py

@@ -93,7 +93,7 @@ class BaseWorkbenchTestCase(WithTestUserTestCase):
                          ).json())))
     namespace: str = None
     hello_world_workflow: Workflow = None
-    engine_param = {
+    engine_params = {
         "id": "presetId",
         "name": "presetName",
         "preset_values": {
@@ -215,7 +215,7 @@ def _create_execution_engine(cls, session: HttpSession) -> ExecutionEngine:
     def _add_execution_engine_parameter(cls, session: HttpSession, engine_id: str) -> EngineParamPreset:
         response = session.post(urljoin(cls.workbench_base_url,
                                         f'/services/ewes-service/{cls.namespace}/engines/{engine_id}/param-presets'),
-                                json=cls.engine_param)
+                                json=cls.engine_params)
         return EngineParamPreset(**response.json())
 
     @classmethod