bugfix: Add missing inputs and outputs in REST API JSON payload (#312)

* Fix logic for fixing missing inputs and outputs

* Fix logic for fixing missing inputs and outputs

* update test ground truth

src/sophios/api/http/restapi.py

@@ -1,7 +1,6 @@
 from pathlib import Path
 import argparse
 import copy
-import uuid
 import yaml
 
 

src/sophios/api/utils/converter.py

@@ -327,45 +327,43 @@ def update_payload_missing_inputs_outputs(wfb_data: Json) -> Json:
     nodes = wfb_data_copy["state"]["nodes"]
     plugins = wfb_data_copy["plugins"]
 
-    # hashmap of node id to nodes for fast node lookup
-    nodes_dict = {node['id']: node for node in nodes}
+    if plugins != []:
+        plugin_config_map: dict[str, dict] = {}
+        plugin_output_map: dict[str, list] = {}
+        for plugin in plugins:
+            pid: str = plugin.get("pid", "")
+            if pid == "":
+                continue
+            plugin_config_map[pid] = get_node_config(plugin)
+            plugin_output_map[pid] = plugin.get("outputs", [])
+
+        # add missing outputs
+        for node in nodes:
+            base_name = node["name"].replace(" ", "").lower() + "_" + str(node["id"])
+            if "outputs" not in node["settings"]:
+                node["settings"]["outputs"] = {}
+            node_outputs = node["settings"]["outputs"]
+            plugin_outputs: list = plugin_output_map.get(node["pluginId"], [])
+            for output in plugin_outputs:
+                if output["type"] == "path" and output["name"] not in node_outputs:
+                    node_outputs[output["name"]] = base_name + "-" + output["name"]
+
+        # hashmap of node id to nodes for fast node lookup
+        nodes_dict = {node['id']: node for node in nodes}
+        # use the look up logic similar to WFB to connect inputs and outputs
+        for link in links:
+            src_node = nodes_dict[link['sourceId']]
+            tgt_node = nodes_dict[link['targetId']]
 
-    # hashmap of plugins id to nodes for fast plugin lookup
-    plugins_dict = {plugin['pid']: plugin for plugin in plugins}
-
-    # find links corresponding to the node
-    for link in links:
-
-        # link ids
-        target_id: int = link["targetId"]
-        source_id: int = link["sourceId"]
-
-        target_node = nodes_dict[target_id]
-        source_node = nodes_dict[source_id]
-
-        # plugins corresponding to the nodes
-        target_plugin = plugins_dict[target_node["pluginId"]]
-        source_plugin = plugins_dict[source_node["pluginId"]]
-
-        def is_inlet(binding: Json) -> bool:
-            """Check if a wfb input is an inlet (directory)"""
-
-            return (
-                binding['type'] in ['directory', 'file', 'path', 'collection', 'csvCollection'] or
-                binding['name'].lower() == 'inpdir' or
-                binding['name'].lower().endswith('path') or
-                binding['name'].lower().endswith('dir')
-            )
-
-        # filter inputs by to only be inlets (directories)
-        input_directories = [binding for binding in target_plugin["inputs"] if is_inlet(binding)]
-        output_directories = [binding for binding in source_plugin["outputs"] if is_inlet(binding)]
-
-        missing_input_key = input_directories[link["inletIndex"]]["name"]
-        missing_output_key = output_directories[link["outletIndex"]]["name"]
+            src_node_ui_config = plugin_config_map.get(src_node['pluginId'], None)
+            tgt_node_ui_config = plugin_config_map.get(tgt_node['pluginId'], None)
 
-        # add the missing input value to the node if needed
-        target_node["settings"]["inputs"][missing_input_key] = source_node["settings"]["outputs"][missing_output_key]
+            if src_node_ui_config and tgt_node_ui_config:
+                inlet_index = link['inletIndex']
+                outlet_index = link['outletIndex']
+                src_node_out_arg = src_node_ui_config['outputs'][outlet_index]["name"]
+                tgt_node_in_arg = tgt_node_ui_config['inputs'][inlet_index]["name"]
+                tgt_node["settings"]["inputs"][tgt_node_in_arg] = src_node["settings"]["outputs"][src_node_out_arg]
 
     if validate_schema_and_object(SCHEMA, wfb_data_copy):
         print('Updated object is valid against input object schema')

tests/data/wfb_data/multi_node/multi_node_wfb_truth.json

@@ -100,8 +100,8 @@
                 "width": 250,
                 "settings": {
                     "inputs": {
-                        "stitchPath": "omeconverter_2-outDir",
-                        "imgPath": "montage_4-outDir"
+                        "stitchPath": "montage_4-outDir",
+                        "imgPath": "omeconverter_2-outDir"
                     },
                     "outputs": {
                         "outDir": "imageassembler_5-outDir"