Merge pull request #23 from InformaticsMatters/sc-3447-job-compliant-variables

Job compliant variables [sc-3447]

Author: alanbchristie

tests/workflow-definitions/duplicate-workflow-variable-names.yaml

@@ -3,7 +3,7 @@ kind: DataManagerWorkflow
 kind-version: "2024.1"
 name: duplicate-workflow-variable-names
 description: A workflow with a duplicate variable name in the input and output
-variables:
+variable-mapping:
   inputs:
   - name: x
     type: squonk/x-smiles

tests/workflow-definitions/simple-python-molprops-with-options.yaml

@@ -3,7 +3,7 @@ kind: DataManagerWorkflow
 kind-version: "2024.1"
 name: python-workflow
 description: A simple python experimental workflow
-variables:
+variable-mapping:
   inputs:
   - name: candidateMolecules
     type: squonk/x-smiles

tests/workflow-definitions/simple-python-molprops.yaml

@@ -3,7 +3,7 @@ kind: DataManagerWorkflow
 kind-version: "2024.1"
 name: python-workflow
 description: A simple python experimental workflow
-variables:
+variable-mapping:
   inputs:
   - name: candidateMolecules
     type: squonk/x-smiles

tests/workflow-definitions/simple-python-parallel.yaml

@@ -3,7 +3,7 @@ kind: DataManagerWorkflow
 kind-version: "2024.1"
 name: python-workflow
 description: A simple branching workflow
-variables:
+variable-mapping:
   inputs:
   - name: candidateMolecules
     type: squonk/x-smiles

tests/workflow-definitions/workflow-options.yaml

@@ -3,7 +3,7 @@ kind: DataManagerWorkflow
 kind-version: "2024.1"
 name: workflow-options
 description: Illustrate the use of workflow options
-variables:
+variable-mapping:
   options:
   - name: variableWithoutDefault
     as:

workflow/decoder.py

@@ -68,7 +68,7 @@ def get_variable_names(definition: dict[str, Any]) -> list[str]:
     outputs and options. This function DOES NOT de-duplicate names,
     that is the role of the validator."""
     wf_variable_names: list[str] = []
-    variables: dict[str, Any] | None = definition.get("variables")
+    variables: dict[str, Any] | None = definition.get("variable-mapping")
     if variables:
         wf_variable_names.extend(
             input_variable["name"] for input_variable in variables.get("inputs", [])
@@ -112,7 +112,7 @@ def set_variables_from_options_for_step(
     assert step_name
 
     result = {}
-    options = definition.get("variables", {}).get("options", [])
+    options = definition.get("variable-mapping", {}).get("options", [])
 
     for opt in options:
         for step_alias in opt["as"]:
@@ -131,7 +131,7 @@ def get_required_variable_names(definition: dict[str, Any]) -> list[str]:
     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")
+    variables: dict[str, Any] | None = definition.get("variable-mapping")
     if variables:
         # All inputs are required (no defaults atm)...
         required_variables.extend(

workflow/workflow-schema.yaml

@@ -28,6 +28,14 @@ properties:
     items:
       $ref: "#/definitions/step"
   variables:
+    # A Job-compliant set of variable declarations for the workflow.
+    # This block structure is a reproduction of that used in Job definitions
+    # and, like JObs, has no current schema.
+    type: object
+    additionalProperties: false
+  variable-mapping:
+    # Workflow-specific variable declarations,
+    # used (at the moment) to map workflow variables to steps.
     type: object
     additionalProperties: false
     properties: