try to fix files not in the same dir problem

app.py

@@ -109,20 +109,20 @@ with gr.Blocks(title="RFD3 Test") as demo:
     display_state = gr.Textbox(label="Selected Batch and Design", visible=True)
     display_state.value = "Please Select a Batch and Design number to show sequence"
     
-    def generate(config_ready, scaffold_ready, num_batches, num_designs_per_batch, config_upload, extra_args):
+    def generate(config_ready, scaffold_ready, config_upload, scaffold_upload, num_batches, num_designs_per_batch, extra_args):
         if config_ready is None or scaffold_ready is None:
             return None, None
         if config_ready == "upload" and scaffold_ready == "no_input":
-            gen_directory, gen_results = generation_with_input_config(config_upload, num_batches, num_designs_per_batch, extra_args)
+            gen_directory, gen_results = generation_with_input_config(config_upload, scaffold_upload num_batches, num_designs_per_batch, extra_args)
             return gen_directory, gen_results
         if config_ready=="upload" and scaffold_ready=="upload":
-            gen_directory, gen_results = generation_with_input_config(config_upload, num_batches, num_designs_per_batch, extra_args)
+            gen_directory, gen_results = generation_with_input_config(config_upload, scaffold_upload, num_batches, num_designs_per_batch, extra_args)
             return gen_directory, gen_results         
         else:
             return None, None
         
     run_btn.click(give_run_status, inputs=[config_ready, scaffold_ready, num_batches, num_designs_per_batch, config_upload, scaffold_upload], outputs=runtextbox).then(
-        generate, inputs=[config_ready, scaffold_ready, num_batches, num_designs_per_batch, config_upload, extra_args], outputs=[gen_directory, gen_results]
+        generate, inputs=[config_ready, scaffold_ready, config_upload, scaffold_upload, num_batches, num_designs_per_batch, extra_args], outputs=[gen_directory, gen_results]
     ).then(
         update_batch_choices,
         inputs=gen_results,

utils/pipelines.py

@@ -8,6 +8,7 @@ import subprocess
 import gzip
 from utils.handle_files import *
 import sys
+import shutil
 
 @spaces.GPU(duration=300)  
 def test_rfd3_from_notebook():
@@ -99,7 +100,7 @@ def unconditional_generation(num_batches, num_designs_per_batch, length):
         raise RuntimeError(f"Error during generation: {str(e)}")
     
 @spaces.GPU(duration=300) 
-def generation_with_input_config(input_file, num_batches, num_designs_per_batch, extra_args):
+def generation_with_input_config(input_file, pdb_file, num_batches, num_designs_per_batch, extra_args):
     """
     Runs an unconditional generation with the specified input config file. Saves the generated structures to a timestamped directory in the outputs folder and returns the path to the directory along with a list of the generated structures' file paths.
 
@@ -107,6 +108,8 @@ def generation_with_input_config(input_file, num_batches, num_designs_per_batch,
     ----------
     input_file: gr.File,
         gr.File object containing the uploaded config file (yaml or json). input_file.name is the path to the uploaded file on the server.
+    pdb_file: gr.File,
+        gr.File object containing the uploaded pdb file for conditioning the generation.
     
     Returns:
     -------
@@ -123,8 +126,16 @@ def generation_with_input_config(input_file, num_batches, num_designs_per_batch,
     os.makedirs(directory, exist_ok=False)
 
     try: 
-        
-        command = f"rfd3 design inputs={input_file} out_dir={directory} n_batches={num_batches} diffusion_batch_size={num_designs_per_batch}"
+        if pdb_file is not None:
+            # I need to do this because uploading files to a HF space stores each file in a separate temp directory so I need to copy them again to the same place.
+            shared_dir = os.mkdir(f"uploads/{time_stamp}_{session_hash}")
+            copied_config_file = os.path.join(shared_dir, os.path.basename(input_file))
+            shutil.copy2(input_file, copied_config_file)
+            copied_pdb_file = os.path.join(shared_dir, os.path.basename(pdb_file))
+            shutil.copy2(pdb_file, copied_pdb_file)
+            command = f"rfd3 design inputs={copied_config_file} out_dir={directory} n_batches={num_batches} diffusion_batch_size={num_designs_per_batch}"
+        else:
+            command = f"rfd3 design inputs={input_file} out_dir={directory} n_batches={num_batches} diffusion_batch_size={num_designs_per_batch}"
         if extra_args:
             command += f" {extra_args}"
         print(f"Running command: {command}")