fix: No longer need realise-outputs

Author: Alan Christie

tests/test_decoder.py

@@ -197,42 +197,6 @@ def test_get_workflow_steps():
     assert steps[1]["name"] == "step2"
 
 
-def test_get_workflow_outputs_for_step_with_name_step1():
-    # Arrange
-
-    # Act
-    has_outputs = decoder.workflow_step_has_outputs(
-        _SIMPLE_PYTHON_MOLPROPS_WITH_OPTIONS_WORKFLOW, "step1"
-    )
-
-    # Assert
-    assert not has_outputs
-
-
-def test_get_workflow_outputs_for_step_with_name_step2():
-    # Arrange
-
-    # Act
-    has_outputs = decoder.workflow_step_has_outputs(
-        _SIMPLE_PYTHON_MOLPROPS_WITH_OPTIONS_WORKFLOW, "step2"
-    )
-
-    # Assert
-    assert has_outputs
-
-
-def test_get_workflow_outputs_for_step_with_unkown_step_name():
-    # Arrange
-
-    # Act
-    has_outputs = decoder.workflow_step_has_outputs(
-        _SIMPLE_PYTHON_MOLPROPS_WITH_OPTIONS_WORKFLOW, "unknown"
-    )
-
-    # Assert
-    assert not has_outputs
-
-
 def test_get_step_input_variable_names_when_duplicates():
     # Arrange
     workflow_filename: str = os.path.join(

tests/test_workflow_validator_for_run_level.py

@@ -156,7 +156,7 @@ def test_validate_simple_python_molprops_with_options_when_missing_required():
     )
 
     # Assert
-    assert error.error_num == 7
+    assert error.error_num == 8
     assert error.error_msg == [
         "Missing workflow variable values for: rdkitPropertyValue"
     ]
@@ -210,7 +210,7 @@ def test_validate_simple_python_molprops_with_missing_input():
     )
 
     # Assert
-    assert error.error_num == 7
+    assert error.error_num == 8
     assert error.error_msg == [
         "Missing workflow variable values for: candidateMolecules"
     ]

workflow/decoder.py

@@ -108,15 +108,6 @@ def get_step_input_variable_names(
     return variable_names
 
 
-def workflow_step_has_outputs(definition: dict[str, Any], name: str) -> bool:
-    """Given a Workflow definition and a step name we return a boolean
-    that is true if the step produces outputs. This requires inspection
-    of the 'as-yet-unused' variables block."""
-    return (
-        len(get_step_output_variable_names(definition=definition, step_name=name)) > 0
-    )
-
-
 def set_step_variables(
     *,
     workflow: dict[str, Any],

workflow/workflow_abc.py

@@ -373,16 +373,6 @@ def get_running_workflow_step_output_values_for_output(
         #   "output": ["dir/file1.sdf", "dir/file2.sdf"]
         # }
 
-    @abstractmethod
-    def realise_outputs(
-        self, *, running_workflow_step_id: str
-    ) -> tuple[dict[str, Any], int]:
-        """Copy (link) the step's files as outputs into the Project directory."""
-        # Should return an empty map or:
-        # {
-        #   "error": "<error message>",
-        # }
-
 
 class MessageDispatcher(ABC):
     """The class handling the sending of messages (on the Data Manager message bus)."""

workflow/workflow_engine.py

@@ -24,7 +24,6 @@
 
 import logging
 import sys
-from http import HTTPStatus
 from pprint import pprint
 from typing import Any, Dict, Optional
 
@@ -44,7 +43,6 @@
     get_step_input_variable_names,
     get_step_replicator,
     set_step_variables,
-    workflow_step_has_outputs,
 )
 
 _LOGGER: logging.Logger = logging.getLogger(__name__)
@@ -250,44 +248,17 @@ def _handle_pod_message(self, msg: PodMessage) -> None:
             self._set_step_error(step_name, r_wfid, r_wfsid, exit_code, "Job failed")
             return
 
-        # If we get here the prior step completed successfully and we can decide
-        # whether the step has outputs (files) that need to be written to the
-        # Project directory, while also marking the Step as DONE (successfully).
-        # We pass the outputs to the DM via a call to the API adapter's realise_outputs().
-        # In return it copies (links) these files to the Project directory.
+        # If we get here the prior step completed successfullyso we
+        # mark the Step as DONE (successfully).
         wfid = rwf_response["workflow"]["id"]
         assert wfid
         wf_response, _ = self._wapi_adapter.get_workflow(workflow_id=wfid)
         _LOGGER.debug("API.get_workflow(%s) returned: -\n%s", wfid, str(wf_response))
 
-        error_num: int | None = None
-        error_msg: str | None = None
-        if workflow_step_has_outputs(wf_response, step_name):
-            # The step produces at least one output.
-            # Inform the DM so it can link them to the Project directory
-            response, status_code = self._wapi_adapter.realise_outputs(
-                running_workflow_step_id=r_wfsid,
-            )
-            if status_code != HTTPStatus.OK:
-                error_num = status_code
-                error_msg = (
-                    response["error"]
-                    if "error" in response
-                    else "Undisclosed error when realising outputs"
-                )
-
-        if error_num is not None:
-            # The job was successful but linking outputs (back to the Project directory)
-            # appears to have failed.
-            self._set_step_error(step_name, r_wfid, r_wfsid, error_num, error_msg)
-            return
-
         # We then inspect the Workflow to determine the next step.
         self._wapi_adapter.set_running_workflow_step_done(
             running_workflow_step_id=r_wfsid,
-            success=error_num is None,
-            error_num=error_num,
-            error_msg=error_msg,
+            success=True,
         )
 
         # We have the step from the Instance that's just finished,

workflow/workflow_validator.py

@@ -153,7 +153,7 @@ def _validate_run_level(
         )
         if missing_values:
             return ValidationResult(
-                error_num=7,
+                error_num=8,
                 error_msg=[
                     f"Missing workflow variable values for: {', '.join(missing_values)}"
                 ],