merge the settings into the main page and better error handling

app.py

@@ -50,38 +50,29 @@ def get_display_state_name(state_key, state_keys):
     else:
         return "_".join(state_key.split("_")[:-1])
 
-def predict_gradio_with_error_handling(
-    file1,
-    file2,
-    pdb_id_input,
-    pdb_file_input,
-    centroid_model,
-    uptake_plots,
-    auto_vmin_vmax,
-    vmin,
-    vmax,
-):
-    """
-    Wrapper function that handles errors and returns error information along with results.
-    """
-    try:
-        # Call the original prediction function
-        results = predict_gradio(
-            file1, file2, pdb_id_input, pdb_file_input, centroid_model,
-            uptake_plots, auto_vmin_vmax, vmin, vmax
-        )
-        return (*results, "", gr.update(visible=False))
-        
-    except Exception as e:
-
-        error_msg = f"Error Type: {type(e).__name__}\n\n"
-        error_msg += f"Error Message: {str(e)}\n\n"
-        error_msg += "Full Traceback:\n"
-        error_msg += traceback.format_exc()
-        
-
-        empty_results = ("", None, "", None, "", None, "", None, None)
-        return (*empty_results, error_msg, gr.update(visible=True))
+def resolve_uploaded_file_path(file_obj):
+    """Normalize Gradio file input into a filesystem path."""
+    if file_obj is None:
+        return None
+    if isinstance(file_obj, str):
+        return file_obj
+    file_name = getattr(file_obj, "name", None)
+    if isinstance(file_name, str):
+        return file_name
+    if isinstance(file_obj, dict):
+        for key in ("name", "path"):
+            value = file_obj.get(key)
+            if isinstance(value, str):
+                return value
+    return None
+
+def get_default_structure_color_range(file1, file2):
+    """Pick structure coloring defaults from the number of HXMS inputs."""
+    has_file1 = resolve_uploaded_file_path(file1) is not None
+    has_file2 = resolve_uploaded_file_path(file2) is not None
+    if has_file1 and has_file2:
+        return -25, 25
+    return 0, 50
 
 def predict_gradio(
     file1,
@@ -90,21 +81,36 @@ def predict_gradio(
     pdb_file_input,
     centroid_model,
     uptake_plots,
-    auto_vmin_vmax,
     vmin,
     vmax,
 ):
 
     print(file1, file2,)
-    if file2 is None:
-        input_files = [file1]
-    else:
-        input_files = [file1, file2]
+    input_files = [
+        resolve_uploaded_file_path(file_obj)
+        for file_obj in (file1, file2)
+    ]
+    input_files = [path for path in input_files if path]
+
+    if len(input_files) == 0:
+        raise gr.Error("Please upload at least one HXMS file.")
+    if vmin is None or vmax is None:
+        vmin, vmax = get_default_structure_color_range(file1, file2)
+    if vmin >= vmax:
+        raise gr.Error("Structure color min must be smaller than structure color max.")
     
     hdxms_data_list = [ load_HXMS_file(input_file) for input_file in input_files ]
     global state_names
     state_names = [state.state_name for data in hdxms_data_list for state in data.states]
     
+    if not centroid_model:
+        _all_tps = [tp for data in hdxms_data_list for state in data.states for pep in state.peptides for tp in pep.timepoints if tp.deut_time != np.inf and tp.deut_time != 0.0]
+        _envelope_tps = [tp for tp in _all_tps if tp.isotope_envelope is not None and len(tp.isotope_envelope) > 3]
+        if len(_envelope_tps) == 0:
+            raise gr.Error(
+                "No envelope data found in the input file(s). "
+                "You may want to use centroid mode or check the input."
+            )
 
     global output_dir
     output_dir = tempfile.mkdtemp()
@@ -147,10 +153,7 @@ def predict_gradio(
     if pdb_id_input or pdb_file_input:
         pdb_path = load_pdb_data(pdb_id_input, pdb_file_input)
         dg_pdb_path = make_BFactorPlot(pdb_path, analysis_objs, output_dir)
-        if auto_vmin_vmax:
-            molstar_view_html = get_structure_html(dg_pdb_path, vmin=vmin, vmax=vmax)
-        else:
-            molstar_view_html = get_structure_html(dg_pdb_path)
+        molstar_view_html = get_structure_html(dg_pdb_path, vmin=vmin, vmax=vmax)
     else:
         molstar_view_html = None
     
@@ -1120,10 +1123,6 @@ def get_colorbar_css(color_list):
         color_stops.append(f"{c} {pct}%")
     return ", ".join(color_stops)
 
-def clear_outputs():
-    """Clear all outputs"""
-    return "", None, "", None, "", None, "", None, None
-
 GA_ID = os.environ.get("GOOGLE_ANALYTICS_ID", "")
 ga_script = ""
 if GA_ID:
@@ -1139,16 +1138,6 @@ if GA_ID:
 
 with gr.Blocks(
     css="""
-    .error-box {
-        background-color: #fee !important;
-        border-left: 4px solid #dc3545 !important;
-        color: #721c24 !important;
-        font-family: monospace !important;
-    }
-    .error-box textarea {
-        background-color: #fee !important;
-        color: #721c24 !important;
-    }
     """,
     head=ga_script
 ) as demo:
@@ -1170,30 +1159,27 @@ with gr.Blocks(
                 with gr.Column(scale=1):
                     demo_btn1 = gr.Button("Load demo data (mini_protein)",)
                     demo_btn2 = gr.Button("Load demo data (ecDHFR)")
-            
-        with gr.TabItem("Settings"):
-            centroid_model = gr.Checkbox(label="Use centroid model", value=False)
-            uptake_plots = gr.Checkbox(label="Generate uptake plots", value=False)
-            
-            with gr.Row():
-                auto_vmin_vmax = gr.Checkbox(label="Custom color range", value=False)
-                vmin = gr.Slider(minimum=-100, maximum=100, value=0, step=1, label="Colorbar minimum")
-                vmax = gr.Slider(minimum=-100, maximum=100, value=50, step=1, label="Colorbar maximum")
+
+            gr.Markdown("### Settings")
+            with gr.Row(equal_height=True):
+                with gr.Column(scale=1, min_width=220):
+                    centroid_model = gr.Checkbox(label="Use centroid model", value=False)
+                    uptake_plots = gr.Checkbox(label="Generate uptake plots", value=False)
+                with gr.Column(scale=1, min_width=220):
+                    with gr.Row():
+                        vmin = gr.Number(
+                            value=0,
+                            label="Structure color min",
+                        )
+                        vmax = gr.Number(
+                            value=50,
+                            label="Structure color max",
+                        )
 
     btn = gr.Button("Run prediction")
 
     gr.Markdown("# Output")
     
-    # Error display
-    error_box = gr.Textbox(
-        label="Error Details", 
-        lines=10, 
-        autoscroll=True, 
-        visible=False,
-        elem_classes=["error-box"],
-        interactive=False
-    )
-    
     with gr.Tabs():
         with gr.TabItem("Summary"):
             summary = gr.Textbox(label="Results summary", lines=30, autoscroll=True)
@@ -1235,11 +1221,7 @@ with gr.Blocks(
             zip_file = gr.File(label="Download all results as a ZIP file")
 
     btn.click(
-        fn=clear_outputs,
-        inputs=[],
-        outputs=[summary, log_kex_plot, molstar_view, uptake_gallery, uptake_info, ae_histogram, ae_info, heatmaps, zip_file],
-    ).then(
-        fn=predict_gradio_with_error_handling,
+        fn=predict_gradio,
         inputs=[
             file1,
             file2,
@@ -1247,19 +1229,46 @@ with gr.Blocks(
             pdb_file_input,
             centroid_model,
             uptake_plots,
-            auto_vmin_vmax,
             vmin,
             vmax,
         ],
-        outputs=[summary, log_kex_plot, molstar_view, uptake_gallery, uptake_info, ae_histogram, ae_info, heatmaps, zip_file, error_box, error_box],
+        outputs=[summary, log_kex_plot, molstar_view, uptake_gallery, uptake_info, ae_histogram, ae_info, heatmaps, zip_file],
     )
 
-    demo_btn1.click(fn=load_demo_data_mini_protein, inputs=[], outputs=[file1, file2, pdb_file_input])
-    demo_btn2.click(fn=load_demo_data_ecDHFR, inputs=[], outputs=[file1, file2, pdb_file_input])
+    file1.change(
+        fn=get_default_structure_color_range,
+        inputs=[file1, file2],
+        outputs=[vmin, vmax],
+    )
+    file2.change(
+        fn=get_default_structure_color_range,
+        inputs=[file1, file2],
+        outputs=[vmin, vmax],
+    )
+
+    demo_btn1.click(
+        fn=load_demo_data_mini_protein,
+        inputs=[],
+        outputs=[file1, file2, pdb_file_input],
+    ).then(
+        fn=get_default_structure_color_range,
+        inputs=[file1, file2],
+        outputs=[vmin, vmax],
+    )
+    demo_btn2.click(
+        fn=load_demo_data_ecDHFR,
+        inputs=[],
+        outputs=[file1, file2, pdb_file_input],
+    ).then(
+        fn=get_default_structure_color_range,
+        inputs=[file1, file2],
+        outputs=[vmin, vmax],
+    )
     
 
 
 demo.launch(
     share=True,
     debug=False,
-)
+    show_error=True,
+)