Merge pull request #15 from InformaticsMatters/prototype-work-alan

Add get_required_variable_names

Author: alanbchristie

workflow/decoder.py

@@ -76,3 +76,17 @@ def get_variable_names(definition: dict[str, Any]) -> list[str]:
             output_variable["name"] for output_variable in variables.get("outputs", [])
         )
     return wf_variable_names
+
+
+def get_required_variable_names(definition: dict[str, Any]) -> list[str]:
+    """Given a Workflow definition this function returns all the names of the
+    variables that are required to be defined when it is RUN - i.e.
+    all those the user needs to provide."""
+    required_variables: list[str] = []
+    variables: dict[str, Any] | None = definition.get("variables")
+    if variables:
+        # For now, all inputs are required...
+        required_variables.extend(
+            input_variable["name"] for input_variable in variables.get("inputs", [])
+        )
+    return required_variables

workflow/workflow-schema.yaml

@@ -84,7 +84,7 @@ definitions:
     - name
     - type
 
-  # An workflow output parameter is essentially a file
+  # A workflow output parameter is essentially a file
   # taken from the output of a step with a default (as) value.
   workflow-output-parameter:
     type: object

workflow/workflow_validator.py

@@ -5,7 +5,12 @@
 from enum import Enum
 from typing import Any
 
-from .decoder import get_steps, get_variable_names, validate_schema
+from .decoder import (
+    get_required_variable_names,
+    get_steps,
+    get_variable_names,
+    validate_schema,
+)
 
 
 class ValidationLevel(Enum):
@@ -153,8 +158,8 @@ def _validate_run_level(
                     error_msg=[f"Specification is missing: {', '.join(missing_keys)}"],
                 )
 
-        # We must have values for all the inputs defined in the workflow.
-        wf_variables: list[str] = get_variable_names(workflow_definition)
+        # We must have values for all the variables defined in the workflow.
+        wf_variables: list[str] = get_required_variable_names(workflow_definition)
         missing_values: list[str] = []
         missing_values.extend(
             wf_variable
@@ -164,7 +169,9 @@ def _validate_run_level(
         if missing_values:
             return ValidationResult(
                 error_num=3,
-                error_msg=[f"Missing input values for: {', '.join(missing_values)}"],
+                error_msg=[
+                    f"Missing workflow variable values for: {', '.join(missing_values)}"
+                ],
             )
 
         return _VALIDATION_SUCCESS