refactor: from-workflow-variable becomes from-workflow

Author: Alan Christie

tests/workflow-definitions/duplicate-step-input-output-variable-names.yaml

@@ -16,10 +16,10 @@ steps:
       value: 123
   variable-mapping:
   - variable: inputFile
-    from-workflow-variable:
+    from-workflow:
       variable: candidateMolecules
   - variable: inputFile
-    from-workflow-variable:
+    from-workflow:
       variable: candidateMolecules
   in:
   - inputFile

tests/workflow-definitions/replicate-using-undeclared-input.yaml

@@ -16,7 +16,7 @@ steps:
       value: 123
   variable-mapping:
   - variable: inputFile
-    from-workflow-variable:
+    from-workflow:
       variable: candidateMolecules
   in:
   - outputFile

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

@@ -17,7 +17,7 @@ steps:
       value: "1"
   variable-mapping:
   - variable: inputFile
-    from-workflow-variable:
+    from-workflow:
       variable: candidateMolecules
 
 - name: parallel-step

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

@@ -62,16 +62,16 @@ steps:
     version: "1.0.0"
   variable-mapping:
   - variable: inputFile
-    from-workflow-variable:
+    from-workflow:
       variable: candidateMolecules
   - variable: name
-    from-workflow-variable:
+    from-workflow:
       variable: rdkitPropertyName
   - variable: value
-    from-workflow-variable:
+    from-workflow:
       variable: rdkitPropertyValue
   - variable: outputFile
-    from-workflow-variable:
+    from-workflow:
       variable: clusteredMolecules
 
 - name: step2
@@ -89,7 +89,7 @@ steps:
       name: step1
       variable: outputFile
   - variable: outputFile
-    from-workflow-variable:
+    from-workflow:
       variable: outputFile
   out:
   - outputFile

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

@@ -16,7 +16,7 @@ steps:
       value: 123
   variable-mapping:
   - variable: inputFile
-    from-workflow-variable:
+    from-workflow:
       variable: candidateMolecules
 
 - name: step2
@@ -34,7 +34,7 @@ steps:
       name: step1
       variable: outputFile
   - variable: outputFile
-    from-workflow-variable:
+    from-workflow:
       variable: clusteredMolecules
   out:
   - outputFile

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

@@ -16,7 +16,7 @@ steps:
       value: "0"
   variable-mapping:
   - variable: inputFile
-    from-workflow-variable:
+    from-workflow:
       variable: candidateMolecules
 
 - name: parallel-step-a

workflow/decoder.py

@@ -73,8 +73,8 @@ def get_workflow_variable_names(definition: dict[str, Any]) -> set[str]:
     for step in steps:
         if v_map := step.get("variable-mapping"):
             for v in v_map:
-                if "from-workflow-variable" in v:
-                    wf_variable_names.add(v["from-workflow-variable"]["variable"])
+                if "from-workflow" in v:
+                    wf_variable_names.add(v["from-workflow"]["variable"])
     return wf_variable_names