fix issue with doc in staticmethods

cwlkernel/cwlrepository/CWLComponent.py

@@ -127,12 +127,14 @@ def steps(self):
         for step in self._steps:
             steps[step] = deepcopy(self._steps[step])
             if not isinstance(steps[step]['run'], str):
-                steps[step]['run'] = f"{steps[step]['run']._id}.cwl"
+                steps[step]['run'] = steps[step]['run'][1]
         return deepcopy(steps)
 
-    def add(self, component: WorkflowComponent, step_name: str) -> None:
+    def add(self, component: WorkflowComponent, step_name: str, run_reference: Optional[str] = None) -> None:
+        if run_reference is None:
+            run_reference = f'{component.id}.cwl'
         self._steps[step_name] = {
-            'run': component,
+            'run': (component, run_reference),
             'in': {},
             'out': []
         }

cwlkernel/cwlrepository/cwlrepository.py

@@ -47,6 +47,9 @@ def get_by_id(self, tool_id: str) -> Optional[WorkflowComponent]:
             comp = self._registry.get(tool_id, None)
             return comp[0] if comp is not None else None
 
+        def get_entry_by_id(self, tool_id: str):
+            return self._registry.get(tool_id, None)
+
         def __iter__(self) -> Iterator[WorkflowComponent]:
             for tool in self._registry.values():
                 yield tool[0]

cwlkernel/kernel_magics.py

@@ -544,14 +544,14 @@ def compile_executed_steps_as_workflow(kernel: CWLKernel, args: str):
     workflow_composer = CWLWorkflow(new_workflow_id)
 
     tools_data_tuples = [
-        (kernel.workflow_repository.get_instance().get_by_id(command.split()[2]), data)
+        (kernel.workflow_repository.get_instance().get_entry_by_id(command.split()[2]), data)
         for command, data in executions_history
     ]
 
-    outputs: Dict[str, List[Dict]] = {out[0].id: out[0].outputs for out in tools_data_tuples}
-
-    for tool, data in tools_data_tuples:  # type: WorkflowComponent, OrderedDict
-        workflow_composer.add(tool, tool.id)
+    outputs: Dict[str, List[Dict]] = {out[0][0].id: out[0][0].outputs for out in tools_data_tuples}
+    repository_root_dir = kernel.workflow_repository.get_instance()._file_repository.ROOT_DIRECTORY
+    for (tool, tools_full_path), data in tools_data_tuples:  # type: WorkflowComponent, OrderedDict
+        workflow_composer.add(tool, tool.id, os.path.relpath(tools_full_path, repository_root_dir))
         for key_id in data:
             if isinstance(data[key_id], dict) and \
                     'class' in data[key_id] and \

examples/githubImport2.ipynb

@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Example on importing a workflow from github"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,