Add result/output node

README.md

@@ -34,25 +34,28 @@ def get_prod_and_div(x: float, y: float) -> dict:
 ```
 These two Python functions are combined in the following example workflow:
 ```python
-tmp_dict = get_prod_and_div(x=1, y=2)
-result = get_sum(x=tmp_dict["prod"], y=tmp_dict["div"])
+def combined_workflow(x=1, y=2):
+    tmp_dict = get_prod_and_div(x=x, y=y)
+    return get_sum(x=tmp_dict["prod"], y=tmp_dict["div"])
 ```
 For the workflow representation of these Python functions the Python functions are stored in the [example_workflows/arithmetic/workflow.py](example_workflows/arithmetic/workflow.py)
 Python module. The connection of the Python functions are stored in the [example_workflows/arithmetic/workflow.json](example_workflows/arithmetic/workflow.json) 
 JSON file:
 ```
 {
   "nodes": [
-    {"id": 0, "function": "simple_workflow.get_prod_and_div"},
-    {"id": 1, "function": "simple_workflow.get_sum"},
-    {"id": 2, "value": 1},
-    {"id": 3, "value": 2}
+    {"id": 0, "type": "function", "value": "workflow.get_prod_and_div"},
+    {"id": 1, "type": "function", "value": "workflow.get_sum"},
+    {"id": 2, "type": "input", "value": 1, "name": "x"},
+    {"id": 3, "type": "input", "value": 2, "name": "y"},
+    {"id": 4, "type": "output", "name": "result"}
   ],
   "edges": [
     {"target": 0, "targetPort": "x", "source": 2, "sourcePort": null},
     {"target": 0, "targetPort": "y", "source": 3, "sourcePort": null},
     {"target": 1, "targetPort": "x", "source": 0, "sourcePort": "prod"},
-    {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"}
+    {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"},
+    {"target": 4, "targetPort": null, "source": 1, "sourcePort": null}
   ]
 }
 ```

documentation/arithmetic.md

@@ -9,25 +9,28 @@ def get_prod_and_div(x: float, y: float) -> dict:
 ```
 These two Python functions are combined in the following example workflow:
 ```python
-tmp_dict = get_prod_and_div(x=1, y=2)
-result = get_sum(x=tmp_dict["prod"], y=tmp_dict["div"])
+def combined_workflow(x=1, y=2):
+    tmp_dict = get_prod_and_div(x=x, y=y)
+    return get_sum(x=tmp_dict["prod"], y=tmp_dict["div"])
 ```
 For the workflow representation of these Python functions the Python functions are stored in the [workflow.py](example_workflows/arithmetic/workflow.py)
 Python module. The connection of the Python functions are stored in the [workflow.json](example_workflows/arithmetic/workflow.json) 
 JSON file:
 ```
 {
   "nodes": [
-    {"id": 0, "function": "workflow.get_prod_and_div"},
-    {"id": 1, "function": "workflow.get_sum"},
-    {"id": 2, "value": 1},
-    {"id": 3, "value": 2}
+    {"id": 0, "type": "function", "value": "workflow.get_prod_and_div"},
+    {"id": 1, "type": "function", "value": "workflow.get_sum"},
+    {"id": 2, "type": "input", "value": 1, "name": "x"},
+    {"id": 3, "type": "input", "value": 2, "name": "y"},
+    {"id": 4, "type": "output", "name": "result"}
   ],
   "edges": [
     {"target": 0, "targetPort": "x", "source": 2, "sourcePort": null},
     {"target": 0, "targetPort": "y", "source": 3, "sourcePort": null},
     {"target": 1, "targetPort": "x", "source": 0, "sourcePort": "prod"},
-    {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"}
+    {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"},
+    {"target": 4, "targetPort": null, "source": 1, "sourcePort": null}
   ]
 }
 ```

example_workflows/arithmetic/workflow.json

@@ -3,12 +3,14 @@
     {"id": 0, "type": "function", "value": "workflow.get_prod_and_div"},
     {"id": 1, "type": "function", "value": "workflow.get_sum"},
     {"id": 2, "type": "input", "value": 1, "name": "x"},
-    {"id": 3, "type": "input", "value": 2, "name": "y"}
+    {"id": 3, "type": "input", "value": 2, "name": "y"},
+    {"id": 4, "type": "output", "name": "result"}
   ],
   "edges": [
     {"target": 0, "targetPort": "x", "source": 2, "sourcePort": null},
     {"target": 0, "targetPort": "y", "source": 3, "sourcePort": null},
     {"target": 1, "targetPort": "x", "source": 0, "sourcePort": "prod"},
-    {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"}
+    {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"},
+    {"target": 4, "targetPort": null, "source": 1, "sourcePort": null}
   ]
 }

example_workflows/nfdi/workflow.json

@@ -6,7 +6,8 @@
     {"id": 3, "type":  "function", "value": "workflow.plot_over_line"},
     {"id": 4, "type": "function", "value": "workflow.substitute_macros"},
     {"id": 5, "type": "function", "value": "workflow.compile_paper"},
-    {"id": 6, "type": "input", "value": 2.0, "name": "domain_size"}
+    {"id": 6, "type": "input", "value": 2.0, "name": "domain_size"},
+    {"id": 7, "type": "output", "name": "result"}
   ],
   "edges": [
     {"target": 0, "targetPort": "domain_size", "source": 6, "sourcePort": null},
@@ -19,6 +20,7 @@
     {"target": 4, "targetPort": "ndofs", "source": 2, "sourcePort": "numdofs"},
     {"target": 4, "targetPort": "domain_size", "source": 6, "sourcePort": null},
     {"target": 5, "targetPort": "macros_tex", "source": 4, "sourcePort": null},
-    {"target": 5, "targetPort": "plot_file", "source": 3, "sourcePort": null}
+    {"target": 5, "targetPort": "plot_file", "source": 3, "sourcePort": null},
+    {"target": 7, "targetPort": null, "source": 5, "sourcePort": null}
   ]
 }

example_workflows/quantum_espresso/workflow.json

@@ -31,7 +31,8 @@
     {"id": 28, "type": "input", "value": "strain_4", "name": "working_directory_5"},
     {"id": 29, "type": "function", "value": "python_workflow_definition.shared.get_dict"},
     {"id": 30, "type": "function", "value": "python_workflow_definition.shared.get_list"},
-    {"id": 31, "type": "function", "value": "python_workflow_definition.shared.get_list"}
+    {"id": 31, "type": "function", "value": "python_workflow_definition.shared.get_list"},
+    {"id": 32, "type": "output", "name": "result"}
   ],
   "edges": [
     {"target": 0, "targetPort": "element", "source": 9, "sourcePort": null},
@@ -92,6 +93,7 @@
     {"target": 31, "targetPort": "2", "source": 5, "sourcePort": "energy"},
     {"target": 31, "targetPort": "3", "source": 6, "sourcePort": "energy"},
     {"target": 31, "targetPort": "4", "source": 7, "sourcePort": "energy"},
-    {"target": 8, "targetPort": "energy_lst", "source": 31, "sourcePort": null}
+    {"target": 8, "targetPort": "energy_lst", "source": 31, "sourcePort": null},
+    {"target": 32, "targetPort": null, "source": 8, "sourcePort": null}
   ]
 }

python_workflow_definition/src/python_workflow_definition/aiida.py

@@ -10,6 +10,8 @@
 from python_workflow_definition.shared import (
     convert_nodes_list_to_dict,
     update_node_names,
+    remove_result,
+    set_result_node,
     NODES_LABEL,
     EDGES_LABEL,
     SOURCE_LABEL,
@@ -21,7 +23,7 @@
 
 def load_workflow_json(file_name: str) -> WorkGraph:
     with open(file_name) as f:
-        data = json.load(f)
+        data = remove_result(workflow_dict=json.load(f))
 
     wg = WorkGraph()
     task_name_mapping = {}
@@ -136,6 +138,10 @@ def write_workflow_json(wg: WorkGraph, file_name: str) -> dict:
                 )
     with open(file_name, "w") as f:
         # json.dump({"nodes": data[], "edges": edges_new_lst}, f)
-        json.dump(update_node_names(content=data), f, indent=2)
+        json.dump(
+            set_result_node(workflow_dict=update_node_names(workflow_dict=data)),
+            f,
+            indent=2,
+        )
 
     return data

python_workflow_definition/src/python_workflow_definition/executorlib.py

@@ -10,6 +10,7 @@
     get_kwargs,
     get_source_handles,
     convert_nodes_list_to_dict,
+    remove_result,
     NODES_LABEL,
     EDGES_LABEL,
     SOURCE_LABEL,
@@ -38,7 +39,7 @@ def _get_value(result_dict: dict, nodes_new_dict: dict, link_dict: dict, exe: Ex
 
 def load_workflow_json(file_name: str, exe: Executor):
     with open(file_name, "r") as f:
-        content = json.load(f)
+        content = remove_result(workflow_dict=json.load(f))
 
     edges_new_lst = content[EDGES_LABEL]
     nodes_new_dict = {}

python_workflow_definition/src/python_workflow_definition/jobflow.py

@@ -12,6 +12,8 @@
     get_source_handles,
     update_node_names,
     convert_nodes_list_to_dict,
+    remove_result,
+    set_result_node,
     NODES_LABEL,
     EDGES_LABEL,
     SOURCE_LABEL,
@@ -271,7 +273,7 @@ def _get_item_from_tuple(input_obj, index, index_lst):
 
 def load_workflow_json(file_name: str) -> Flow:
     with open(file_name, "r") as f:
-        content = json.load(f)
+        content = remove_result(workflow_dict=json.load(f))
 
     edges_new_lst = []
     for edge in content[EDGES_LABEL]:
@@ -332,8 +334,10 @@ def write_workflow_json(flow: Flow, file_name: str = "workflow.json"):
 
     with open(file_name, "w") as f:
         json.dump(
-            update_node_names(
-                content={NODES_LABEL: nodes_store_lst, EDGES_LABEL: edges_lst}
+            set_result_node(
+                workflow_dict=update_node_names(
+                    workflow_dict={NODES_LABEL: nodes_store_lst, EDGES_LABEL: edges_lst}
+                )
             ),
             f,
             indent=2,

python_workflow_definition/src/python_workflow_definition/plot.py

@@ -39,7 +39,10 @@ def plot(file_name: str):
                     k + "=result[" + v[SOURCE_PORT_LABEL] + "]"
                 )
         for k, v in edge_label_dict.items():
-            graph.add_edge(str(k), str(target_node), label=", ".join(v))
+            if len(v) == 1 and v[0] is not None:
+                graph.add_edge(str(k), str(target_node), label=", ".join(v))
+            else:
+                graph.add_edge(str(k), str(target_node))
 
     svg = nx.nx_agraph.to_agraph(graph).draw(prog="dot", format="svg")
     display(SVG(svg))

python_workflow_definition/src/python_workflow_definition/purepython.py

@@ -9,6 +9,7 @@
     get_kwargs,
     get_source_handles,
     convert_nodes_list_to_dict,
+    remove_result,
     NODES_LABEL,
     EDGES_LABEL,
     SOURCE_LABEL,
@@ -67,7 +68,7 @@ def _get_value(result_dict: dict, nodes_new_dict: dict, link_dict: dict):
 
 def load_workflow_json(file_name: str):
     with open(file_name, "r") as f:
-        content = json.load(f)
+        content = remove_result(workflow_dict=json.load(f))
 
     edges_new_lst = content[EDGES_LABEL]
     nodes_new_dict = {}

python_workflow_definition/src/python_workflow_definition/pyiron_base.py

@@ -12,6 +12,8 @@
     get_source_handles,
     convert_nodes_list_to_dict,
     update_node_names,
+    remove_result,
+    set_result_node,
     NODES_LABEL,
     EDGES_LABEL,
     SOURCE_LABEL,
@@ -229,7 +231,7 @@ def load_workflow_json(file_name: str, project: Optional[Project] = None):
         project = Project(".")
 
     with open(file_name, "r") as f:
-        content = json.load(f)
+        content = remove_result(workflow_dict=json.load(f))
 
     edges_new_lst = content[EDGES_LABEL]
     nodes_new_dict = {}
@@ -293,8 +295,13 @@ def write_workflow_json(
 
     with open(file_name, "w") as f:
         json.dump(
-            update_node_names(
-                content={NODES_LABEL: nodes_store_lst, EDGES_LABEL: edges_new_lst}
+            set_result_node(
+                workflow_dict=update_node_names(
+                    workflow_dict={
+                        NODES_LABEL: nodes_store_lst,
+                        EDGES_LABEL: edges_new_lst,
+                    }
+                )
             ),
             f,
             indent=2,

python_workflow_definition/src/python_workflow_definition/shared.py

@@ -42,19 +42,20 @@ def get_source_handles(edges_lst: list) -> dict:
 
 def convert_nodes_list_to_dict(nodes_list: list) -> dict:
     return {
-        str(el["id"]): el["value"] for el in sorted(nodes_list, key=lambda d: d["id"])
+        str(el["id"]): el["value"] if "value" in el else el["name"]
+        for el in sorted(nodes_list, key=lambda d: d["id"])
     }
 
 
-def update_node_names(content: dict) -> dict:
+def update_node_names(workflow_dict: dict) -> dict:
     node_names_final_dict = {}
-    input_nodes = [n for n in content[NODES_LABEL] if n["type"] == "input"]
+    input_nodes = [n for n in workflow_dict[NODES_LABEL] if n["type"] == "input"]
     node_names_dict = {
         n["id"]: list(
             set(
                 [
                     e[TARGET_PORT_LABEL]
-                    for e in content[EDGES_LABEL]
+                    for e in workflow_dict[EDGES_LABEL]
                     if e[SOURCE_LABEL] == n["id"]
                 ]
             )
@@ -71,7 +72,44 @@ def update_node_names(content: dict) -> dict:
         else:
             node_names_final_dict[k] = v
 
-    for n in content[NODES_LABEL]:
+    for n in workflow_dict[NODES_LABEL]:
         if n["type"] == "input":
             n["name"] = node_names_final_dict[n["id"]]
-    return content
+    return workflow_dict
+
+
+def set_result_node(workflow_dict):
+    node_id_lst = [n["id"] for n in workflow_dict[NODES_LABEL]]
+    source_lst = list(set([e[SOURCE_LABEL] for e in workflow_dict[EDGES_LABEL]]))
+
+    end_node_lst = []
+    for ni in node_id_lst:
+        if ni not in source_lst:
+            end_node_lst.append(ni)
+
+    node_id = len(workflow_dict[NODES_LABEL])
+    workflow_dict[NODES_LABEL].append(
+        {"id": node_id, "type": "output", "name": "result"}
+    )
+    workflow_dict[EDGES_LABEL].append(
+        {
+            TARGET_LABEL: node_id,
+            TARGET_PORT_LABEL: None,
+            SOURCE_LABEL: end_node_lst[0],
+            SOURCE_PORT_LABEL: None,
+        }
+    )
+
+    return workflow_dict
+
+
+def remove_result(workflow_dict):
+    node_output_id = [
+        n["id"] for n in workflow_dict[NODES_LABEL] if n["type"] == "output"
+    ][0]
+    return {
+        NODES_LABEL: [n for n in workflow_dict[NODES_LABEL] if n["type"] != "output"],
+        EDGES_LABEL: [
+            e for e in workflow_dict[EDGES_LABEL] if e[TARGET_LABEL] != node_output_id
+        ],
+    }