cwl: fix workflow serialization

renga/cli/_graph.py

@@ -29,6 +29,7 @@
 from renga._compat import Path
 from renga.api import LocalClient
 from renga.models.cwl.command_line_tool import CommandLineTool
+from renga.models.cwl.parameter import InputParameter, WorkflowOutputParameter
 from renga.models.cwl.workflow import Workflow
 
 
@@ -297,11 +298,13 @@ def ascwl(self):
                 input_mapping = ins.get(input_.id)
                 if input_mapping is None:
                     input_id = 'input_{0}'.format(input_index)
-                    workflow.inputs.append({
-                        'id': input_id,
-                        'type': input_.type,
-                        'default': input_.default,
-                    })
+                    workflow.inputs.append(
+                        InputParameter(
+                            id=input_id,
+                            type=input_.type,
+                            default=input_.default,
+                        )
+                    )
                     input_index += 1
                     ins[input_.id] = input_id
 
@@ -314,10 +317,12 @@ def ascwl(self):
 
         for index, key in enumerate(self._output_keys):
             output_id = 'output_{0}'.format(index)
-            workflow.outputs.append({
-                'id': output_id,
-                'type': 'File',
-                'outputSource': self._source_name(key),
-            })
+            workflow.outputs.append(
+                WorkflowOutputParameter(
+                    id=output_id,
+                    type='File',
+                    outputSource=self._source_name(key),
+                )
+            )
 
         return workflow

renga/models/cwl/parameter.py

@@ -22,6 +22,37 @@
 from .types import File
 
 
+def convert_default(value):
+    """Convert a default value."""
+    if isinstance(value, dict):
+        return File.from_cwl(value)
+    return value
+
+
+@attr.s
+class _IdMixin(object):
+    """Define id field."""
+
+    id = attr.ib()
+
+
+@attr.s
+class Parameter(object):
+    """Define an input or output parameter to a process."""
+
+    streamable = attr.ib(default=None, converter=bool)
+
+
+@attr.s
+class InputParameter(_IdMixin, Parameter):
+    """An input parameter."""
+
+    type = attr.ib(default='string')
+    description = attr.ib(default=None)
+    default = attr.ib(default=None, converter=convert_default)
+    inputBinding = attr.ib(default=None)
+
+
 @attr.s
 class CommandLineBinding(object):
     """Define the binding behavior when building the command line."""
@@ -34,28 +65,26 @@ class CommandLineBinding(object):
     shellQuote = attr.ib(default=True, type=bool)
 
 
-def convert_default(value):
-    """Convert a default value."""
-    if isinstance(value, dict):
-        return File.from_cwl(value)
-    return value
-
-
 @attr.s
-class CommandInputParameter(object):
+class CommandInputParameter(InputParameter):
     """An input parameter for a CommandLineTool."""
 
-    id = attr.ib()
-    type = attr.ib(default='string')
-    description = attr.ib(default=None)
-    default = attr.ib(default=None, converter=convert_default)
     inputBinding = attr.ib(
         default=None,
         converter=lambda data: CommandLineBinding(**data) if not isinstance(
             data, CommandLineBinding
         ) and data is not None else data,
     )
-    streamable = attr.ib(default=None)
+
+
+@attr.s
+class OutputParameter(_IdMixin, Parameter):
+    """An output parameter."""
+
+    type = attr.ib(default='string')
+    description = attr.ib(default=None)
+    format = attr.ib(default=None)
+    outputBinding = attr.ib(default=None)
 
 
 @attr.s
@@ -67,17 +96,19 @@ class CommandOutputBinding(object):
 
 
 @attr.s
-class CommandOutputParameter(object):
-    """An input parameter for a CommandLineTool."""
+class CommandOutputParameter(OutputParameter):
+    """Define an output parameter for a CommandLineTool."""
 
-    id = attr.ib()
-    type = attr.ib(default='string')
-    description = attr.ib(default=None)
-    format = attr.ib(default=None)
     outputBinding = attr.ib(
         default=None,
         converter=lambda data: CommandOutputBinding(**data) if not isinstance(
             data, CommandOutputBinding
         ) and data is not None else data,
     )
-    streamable = attr.ib(default=None)
+
+
+@attr.s
+class WorkflowOutputParameter(OutputParameter):
+    """Define an output parameter for a Workflow."""
+
+    outputSource = attr.ib(default=None)

renga/models/cwl/process.py

@@ -19,27 +19,16 @@
 
 import attr
 
+from ._ascwl import mapped
+from .parameter import InputParameter, OutputParameter
+
 
 @attr.s(init=False)
 class Process(object):
     """Represent a process."""
 
-    inputs = attr.ib(
-        default=attr.Factory(list),
-        metadata={
-            'jsonldPredicate': {
-                'mapSubject': 'id'
-            },
-        }
-    )  # list InputParameter
-    outputs = attr.ib(
-        default=attr.Factory(list),
-        metadata={
-            'jsonldPredicate': {
-                'mapSubject': 'id'
-            },
-        }
-    )  # list OutputParameter
+    inputs = mapped(InputParameter)
+    outputs = mapped(OutputParameter)
     requirements = attr.ib(default=attr.Factory(list))
     # list ProcessRequirement
     hints = attr.ib(default=attr.Factory(list))  # list Any

renga/models/cwl/workflow.py

@@ -22,6 +22,7 @@
 import attr
 
 from ._ascwl import CWLClass, mapped
+from .parameter import WorkflowOutputParameter
 from .process import Process
 
 
@@ -40,6 +41,7 @@ class WorkflowStep(object):
 class Workflow(Process, CWLClass):
     """Define a workflow representation."""
 
+    outputs = mapped(WorkflowOutputParameter)
     steps = mapped(WorkflowStep)
 
     def add_step(self, **kwargs):