remove deprecated gr.File.name attribute

app.py

@@ -130,7 +130,7 @@ with gr.Blocks(title="RFD3 Test") as demo:
             gen_directory, gen_results = unconditional_generation(num_batches, num_designs_per_batch, length)
             return gen_directory, gen_results
         
-    run_btn.click(give_run_status, inputs=[config_ready, scaffold_ready, num_batches, num_designs_per_batch, length], outputs=runtextbox).then(
+    run_btn.click(give_run_status, inputs=[config_ready, scaffold_ready, num_batches, num_designs_per_batch, length, config_upload], outputs=runtextbox).then(
         generate, inputs=[config_ready, scaffold_ready, num_batches, num_designs_per_batch, length], outputs=[gen_directory, gen_results]
     ).then(
         update_batch_choices,

utils/handle_events.py

@@ -1,4 +1,5 @@
 import gradio as gr
+from utils.handle_files import *
 
 def update_batch_choices(result):
     """
@@ -106,7 +107,7 @@ def validate_scaffold_ready_with_file(scaffold_upload):
     else:
         return "Please upload a scaffold file or press 'No Scaffold/Target' for unconditional generation.", None
     
-def give_run_status(config_ready, scaffold_ready, num_batches, num_designs_per_batch, length):
+def give_run_status(config_ready, scaffold_ready, num_batches, num_designs_per_batch, length, config_upload):
     """
     Once the user presses on the Run Generation button, this function checks whether both config and scaffold are ready, and gives a status message about the generation run that is about to happen. If both config and scaffold are not ready, it prompts the user to ensure they are both validated before running the generation.
 
@@ -122,6 +123,8 @@ def give_run_status(config_ready, scaffold_ready, num_batches, num_designs_per_b
         number of designs per batch input by the user in the manual config, used for the generation
     length: gr.Number
         length input by the user in the manual config, used for the generation status message
+    config_upload: gr.File
+        uploaded config file, used for the generation status message if upload config is selected
 
     Returns:
     -------
@@ -133,5 +136,7 @@ def give_run_status(config_ready, scaffold_ready, num_batches, num_designs_per_b
         return gr.update(value="Please ensure both config and scaffold are validated before running the generation.")
     elif config_ready=="manual" and scaffold_ready=="no_input":
         return gr.update(value=f"Running unconditional generation with minimal configuration: {num_batches} batches of {num_designs_per_batch} designs each, length = {length} aa")
+    elif config_ready == "upload" and scaffold_ready == "no_input":
+        return gr.update(value=f"Running unconditional generation with uploaded config file {config_upload}")
     else:
         return gr.update(value=f"Not implemented yet")

utils/handle_files.py

@@ -3,6 +3,9 @@ import os
 import shutil
 import gradio as gr
 import subprocess
+import json
+import yaml
+from pathlib import Path
 
 def mcif_gz_to_pdb(file_path: str) -> str:
     """
@@ -50,4 +53,33 @@ def collect_outputs(gen_directory, num_batches, num_designs_per_batch):
         file_list = subprocess.check_output(cmd, shell=True).decode()
         return file_list
     except Exception as e:
-        return f"Error: {str(e)}"
+        return f"Error: {str(e)}"
+    
+
+def load_config(file_path: str | Path) -> dict | list:
+    """
+    Load YAML or JSON file into a Python object.
+    
+    Args:
+        file_path: Path to the YAML or JSON file.
+    
+    Returns:
+        Parsed Python object (dict, list, etc.).
+    
+    Raises:
+        ValueError: If extension is not .yaml, .yml, or .json.
+        Exception: On parse errors.
+    """
+    path = Path(file_path)
+    if not path.exists():
+        raise FileNotFoundError(f"File not found: {file_path}")
+    
+    ext = path.suffix.lower()
+    if ext in {'.yaml', '.yml'}:
+        with open(path, 'r', encoding='utf-8') as f:
+            return yaml.safe_load(f)  # Secure loader [web:1][web:4]
+    elif ext == '.json':
+        with open(path, 'r', encoding='utf-8') as f:
+            return json.load(f)  # Built-in JSON loader [web:12]
+    else:
+        raise ValueError(f"Unsupported extension: {ext}. Use .yaml, .yml, or .json.")

utils/pipelines.py

@@ -124,7 +124,7 @@ def unconditional_generation_with_input_config(input_file):
 
     try: 
         
-        command = f"rfd3 design inputs={input_file.name} out_dir={directory}"
+        command = f"rfd3 design inputs={input_file} out_dir={directory}"
         print(f"Running command: {command}")
         subprocess.run(command, shell=True, check=True)