Core refactor (HTML download, code cleanup, plot caching)

app.py

@@ -116,6 +116,7 @@ def server(input, output, session):
 
     shared = {
         "preloaded_data": preloaded_data,  # Preloaded data for initial load
+        "preloaded_file_path": file_path,  # Path to preloaded file for filename extraction
         "data_loaded": data_loaded,  # Reactive to track if data is loaded
         "adata_main": adata_main,  # Main anndata object
     }
@@ -124,6 +125,11 @@ def server(input, output, session):
     # and add them to the shared dictionary
     for key in data_keys:
         shared[key] = reactive.Value(None)
+
+    # Add reactive value for input filename
+    shared['input_filename'] = reactive.Value(None)
+    shared['boxplot_fig'] = reactive.Value(None)
+    shared['sankey_fig'] = reactive.Value(None)
 
     # Individual server components
     getting_started_server(input, output, session, shared)

server/anno_vs_anno_server.py

@@ -11,50 +11,94 @@ def anno_vs_anno_server(input, output, session, shared):
     @reactive.event(input.go_sk1, ignore_none=True)
     def spac_Sankey():
         adata = ad.AnnData(
-            X=shared['X_data'].get(), 
-            obs=pd.DataFrame(shared['obs_data'].get()), 
-            layers=shared['layers_data'].get(), 
+            X=shared['X_data'].get(),
+            obs=pd.DataFrame(shared['obs_data'].get()),
+            layers=shared['layers_data'].get(),
             dtype=shared['X_data'].get().dtype
         )
-        if adata is not None:
-            fig = spac.visualization.sankey_plot(
-                adata, 
-                source_annotation=input.sk1_anno1(), 
-                target_annotation=input.sk1_anno2()
-            )
-            return fig
-        return None
+        if adata is None:
+            return None
+        fig = spac.visualization.sankey_plot(
+            adata,
+            source_annotation=input.sk1_anno1(),
+            target_annotation=input.sk1_anno2()
+        )
+        shared['sankey_fig'].set(fig)  # Store figure for HTML download
+        return fig
 
     @output
     @render_widget
     @reactive.event(input.go_rhm1, ignore_none=True)
     def spac_Relational():
         adata = ad.AnnData(
-            X=shared['X_data'].get(), 
+            X=shared['X_data'].get(),
             obs=pd.DataFrame(shared['obs_data'].get())
         )
-        if adata is not None:
-            result = spac.visualization.relational_heatmap(
-                adata, 
-                source_annotation=input.rhm_anno1(), 
-                target_annotation=input.rhm_anno2()
-            )
-            shared['df_relational'].set(result['data'])
-            return result['figure']
-        return None
+        if adata is None:
+            return None
+        result = spac.visualization.relational_heatmap(
+            adata,
+            source_annotation=input.rhm_anno1(),
+            target_annotation=input.rhm_anno2()
+        )
+        shared['df_relational'].set(result['data'])
+        return result['figure']
+
 
     @render.download(filename="relational_data.csv")
     def download_df_1():
         df = shared['df_relational'].get()
-        if df is not None:
-            csv_string = df.to_csv(index=False)
-            csv_bytes = csv_string.encode("utf-8")
-            return csv_bytes, "text/csv"
-        return None
+        if df is None:
+            return None
+        csv_string = df.to_csv(index=False)
+        csv_bytes = csv_string.encode("utf-8")
+        return csv_bytes, "text/csv"
+
 
     @render.ui
     @reactive.event(input.go_rhm1, ignore_none=True)
     def download_button_ui_1():
-        if shared['df_relational'].get() is not None:
-            return ui.download_button("download_df_1", "Download Data", class_="btn-warning")
-        return None
+        if shared['df_relational'].get() is None:
+            return None
+        return ui.download_button("download_df_1", "Download Data", class_="btn-warning")
+
+    def get_sankey_html_filename():
+        """Generate HTML download filename for sankey."""
+        input_filename = shared['input_filename'].get()
+        if input_filename:
+            return f"{input_filename}_sankey.html"
+        return "sankey.html"
+
+    @render.download(filename=get_sankey_html_filename)
+    def download_sankey_html():
+        fig = shared['sankey_fig'].get()
+        if fig is None:
+            return None
+        html_string = fig.to_html(include_plotlyjs='cdn')
+        html_bytes = html_string.encode("utf-8")
+        return html_bytes, "text/html"
+
+    @render.ui
+    @reactive.event(input.go_sk1, ignore_none=True)
+    def download_button_ui_sankey():
+        if shared['sankey_fig'].get() is None:
+            return None
+        return ui.input_action_button(
+            "show_download_modal_sankey",
+            "Download Data",
+            class_="btn-warning"
+        )
+
+    @reactive.Effect
+    @reactive.event(input.show_download_modal_sankey)
+    def show_download_modal_sankey():
+        m = ui.modal(
+            ui.div(
+                ui.download_button("download_sankey_html", "HTML", class_="btn-primary"),
+                style="display: flex; gap: 10px; justify-content: center;"
+            ),
+            title="Select a Format:",
+            easy_close=True,
+            footer=None
+        )
+        ui.modal_show(m)

server/annotations_server.py

@@ -17,24 +17,24 @@ def spac_Histogram_2():
                 adata,
                 annotation=input.h2_anno()
             ).values()
-            shared['df_histogram2'].set(df) 
+            shared['df_histogram2'].set(df)
             ax.tick_params(axis='x', rotation=input.anno_slider(), labelsize=10)
             return fig
 
-        # 2) If "Group By" is CHECKED, we must always supply a 
+        # 2) If "Group By" is CHECKED, we must always supply a
         #    valid multiple parameter
         else:
-            # If user also checked "Plot Together", use their selected 
+            # If user also checked "Plot Together", use their selected
             # stack type
             if input.h2_together_check():
                 # e.g. 'stack', 'dodge', etc.
-                multiple_param = input.h2_together_drop()  
+                multiple_param = input.h2_together_drop()
 
                 together_flag = True
             else:
                 # If grouping by but not "plot together", pick a default layout
                 # or 'dodge' or any valid string
-                multiple_param = "layer"  
+                multiple_param = "layer"
                 together_flag = False
 
             fig, ax, df = spac.visualization.histogram(
@@ -44,12 +44,12 @@ def spac_Histogram_2():
                 together=together_flag,
                 multiple=multiple_param
             ).values()
-            shared['df_histogram2'].set(df) 
+            shared['df_histogram2'].set(df)
             axes = ax if isinstance(ax, (list, np.ndarray)) else [ax]
             for ax in axes:
                 ax.tick_params(
-                    axis='x', 
-                    rotation=input.anno_slider(), 
+                    axis='x',
+                    rotation=input.anno_slider(),
                     labelsize=10
                 )
             return fig
@@ -59,23 +59,24 @@ def spac_Histogram_2():
     @render.ui
     @reactive.event(input.go_h2, ignore_none=True)
     def download_histogram_button_ui():
-        if shared['df_histogram2'].get() is not None:
-            return ui.download_button(
-                "download_histogram2_df", 
-                "Download Data", 
-                class_="btn-warning"
-            )
-        return None
+        if shared['df_histogram2'].get() is None:
+            return None
+        return ui.download_button(
+            "download_histogram2_df",
+            "Download Data",
+            class_="btn-warning"
+        )
+
 
 
     @render.download(filename="annotation_histogram_data.csv")
     def download_histogram2_df():
         df = shared['df_histogram2'].get()
-        if df is not None:
-            csv_string = df.to_csv(index=False)
-            csv_bytes = csv_string.encode("utf-8")
-            return csv_bytes, "text/csv"
-        return None
+        if df is None:
+            return None
+        csv_string = df.to_csv(index=False)
+        csv_bytes = csv_string.encode("utf-8")
+        return csv_bytes, "text/csv"
 
     histogram2_ui_initialized = reactive.Value(False)
 
@@ -86,8 +87,8 @@ def histogram_reactivity_2():
 
         if btn and not ui_initialized:
             dropdown = ui.input_select(
-                "h2_anno_1", 
-                "Select an Annotation", 
+                "h2_anno_1",
+                "Select an Annotation",
                 choices=shared['obs_names'].get()
             )
             ui.insert_ui(
@@ -97,8 +98,8 @@ def histogram_reactivity_2():
             )
 
             together_check = ui.input_checkbox(
-                "h2_together_check", 
-                "Plot Together", 
+                "h2_together_check",
+                "Plot Together",
                 value=True
             )
             ui.insert_ui(
@@ -120,18 +121,18 @@ def histogram_reactivity_2():
     def update_stack_type_dropdown():
         if input.h2_together_check():
             dropdown_together = ui.input_select(
-                "h2_together_drop", 
-                "Select Stack Type", 
-                choices=['stack', 'layer', 'dodge', 'fill'], 
+                "h2_together_drop",
+                "Select Stack Type",
+                choices=['stack', 'layer', 'dodge', 'fill'],
                 selected='stack'
             )
             ui.insert_ui(
                 ui.div({
-                    "id": "inserted-dropdown_together-1"}, 
+                    "id": "inserted-dropdown_together-1"},
                     dropdown_together
                 ),
                 selector="#main-h2_together_drop",
                 where="beforeEnd"
-            )      
+            )
         else:
             ui.remove_ui("#inserted-dropdown_together-1")