Added workflows folder and utils.py to support workflow generation

workflows/utils.py

@@ -0,0 +1,107 @@
+import yaml
+import os
+from collections import OrderedDict
+
+def generate_command(base_command='python', inputs=None, outputs=None, parameters=None):
+    inputs = inputs or []
+    outputs = outputs or []
+    placeholders = [
+        f"${name}"
+        for name, value in inputs + parameters + outputs
+        if isinstance(value, dict) and not value.get('implicit', False)
+    ]
+    return f"{base_command} {' '.join(placeholders)}"
+
+class RenkuWorkflowBuilder:
+    def __init__(self, name):
+        self.name = name
+        self.steps = OrderedDict()
+
+    def add_step(self, step_name, base_command, inputs=None, outputs=None, parameters=None):
+        command = generate_command(base_command, inputs, outputs,parameters)
+        step = {
+            'command': command
+        }
+        if inputs:
+            step['inputs'] = [{key: value} for key, value in inputs]
+        if outputs:
+            step['outputs'] = [{key: value} for key, value in outputs]
+        if parameters:
+            step['parameters'] = [{key: value} for key, value in parameters] 
+        self.steps[step_name] = step
+
+    @staticmethod
+    def parse_workflow(yaml_content: str):
+        data = yaml.safe_load(yaml_content)
+        builder = RenkuWorkflowBuilder(data['name'])
+
+        for step_name, step_def in data['steps'].items():
+            command = step_def.get('command')
+            inputs = step_def.get('inputs', [])
+            outputs = step_def.get('outputs', [])
+            parameters = step_def.get('parameters', [])
+            builder.steps[step_name] = {
+                'command': command,
+                'inputs': inputs,
+                'outputs': outputs,
+                'parameters': parameters
+            }
+        return builder
+
+    @staticmethod
+    def from_file(filepath):
+        if not os.path.exists(filepath):
+            return None
+        with open(filepath, 'r') as f:
+            return RenkuWorkflowBuilder.parse_workflow(f.read())
+
+    def to_dict(self):
+        for step_name, step_value in self.steps.items():
+            for segment in ['inputs','outputs']:
+                for item in step_value.get(segment,[]):# ['inputs', 'outputs']:
+                    # Go over either inputs or outputs
+                    for name, value in item.items():
+                        if not isinstance(value, dict):
+                            raise ValueError(f"Invalid input. Step {step_name} must have {segment} of either dict or str type.")
+                        if isinstance(value, str):
+                            continue
+                        if isinstance(value, dict) and 'path' in value.keys():
+                            value['path'] = value['path'].replace(os.sep, '/')
+
+        return {
+            'name': self.name,
+            'steps': { key : value for key, value in self.steps.items()}
+        }
+
+    def to_yaml(self):
+        return yaml.dump(self.to_dict(), sort_keys=False)
+
+    def append_from(self, other, force=False):
+        if other.name != self.name:
+            raise ValueError(f"Cannot merge workflows with different names: {self.name} != {other.name}")
+
+        for step_name, step_def in other.steps.items():
+            if step_name in self.steps:
+                if force:
+                    print(f"[Overwriting] Step '{step_name}' was overwritten as 'force=True'.")
+                    self.steps[step_name] = step_def
+                else:
+                    print(f"[Skipping] Step '{step_name}' already exists. Use 'force=True' to overwrite.")
+            else:
+                self.steps[step_name] = step_def
+
+    def save_to_file(self, directory):
+        os.makedirs(directory, exist_ok=True)
+        filepath = os.path.join(directory, f"{self.name}.yaml")
+
+        if os.path.exists(filepath):
+            existing = RenkuWorkflowBuilder.from_file(filepath)
+            if existing and existing.name == self.name:
+                existing.append_from(self)
+                with open(filepath, 'w') as f:
+                    f.write(existing.to_yaml())
+                return
+        # Save as new
+        with open(filepath, 'w') as f:
+            f.write(self.to_yaml())
+