changes from todays meeting

webapp/app/main.py

@@ -107,23 +107,51 @@ if static_path.exists():
 
 # Mount PyShiny visualization apps
 if SHINY_AVAILABLE:
-    # Use dynamic port from settings (7860 for HF Spaces/Docker, can be overridden via env)
-    api_base_url = f"http://localhost:{settings.server_port}"
+    # For server-side requests within the same process, use 127.0.0.1 with the configured port
+    # The PyShiny apps make server-side HTTP requests to fetch data
+    api_base_url = f"http://127.0.0.1:{settings.server_port}"
     logger.info(f"Configuring Shiny apps with API base URL: {api_base_url}")
+    logger.info(f"Server port from settings: {settings.server_port}")
 
     try:
-        heatmap_shiny_app = create_heatmap_app(api_base_url=api_base_url)
-        app.mount("/shiny/heatmap", heatmap_shiny_app, name="shiny_heatmap")
-        logger.info("PyShiny heatmap app mounted at /shiny/heatmap")
+        heatmap_shiny_app = create_heatmap_app(api_base_url=api_base_url, fastapi_app=app)
+        logger.info(f"Heatmap app created: {type(heatmap_shiny_app)}")
+        # Try mounting the PyShiny App directly first (it's ASGI-compatible)
+        # If that doesn't work, fall back to starlette_app
+        try:
+            app.mount("/shiny/heatmap", heatmap_shiny_app, name="shiny_heatmap")
+            logger.info("PyShiny heatmap app mounted directly at /shiny/heatmap")
+        except Exception as mount_error:
+            logger.warning(f"Direct mount failed, trying starlette_app: {mount_error}")
+            starlette_app = heatmap_shiny_app.starlette_app
+            app.mount("/shiny/heatmap", starlette_app, name="shiny_heatmap")
+            logger.info("PyShiny heatmap app mounted via starlette_app at /shiny/heatmap")
     except Exception as e:
         logger.error(f"Failed to mount PyShiny heatmap app: {e}")
+        import traceback
+        traceback.print_exc()
 
     try:
-        silhouette_shiny_app = create_silhouette_app(api_base_url=api_base_url)
-        app.mount("/shiny/silhouette", silhouette_shiny_app, name="shiny_silhouette")
-        logger.info("PyShiny silhouette app mounted at /shiny/silhouette")
+        silhouette_shiny_app = create_silhouette_app(api_base_url=api_base_url, fastapi_app=app)
+        logger.info(f"Silhouette app created: {type(silhouette_shiny_app)}")
+        # Try mounting the PyShiny App directly first (it's ASGI-compatible)
+        # If that doesn't work, fall back to starlette_app
+        try:
+            app.mount("/shiny/silhouette", silhouette_shiny_app, name="shiny_silhouette")
+            logger.info("PyShiny silhouette app mounted directly at /shiny/silhouette")
+        except Exception as mount_error:
+            logger.warning(f"Direct mount failed, trying starlette_app: {mount_error}")
+            starlette_app = silhouette_shiny_app.starlette_app
+            app.mount("/shiny/silhouette", starlette_app, name="shiny_silhouette")
+            logger.info("PyShiny silhouette app mounted via starlette_app at /shiny/silhouette")
     except Exception as e:
         logger.error(f"Failed to mount PyShiny silhouette app: {e}")
+        import traceback
+        traceback.print_exc()
+else:
+    logger.warning("PyShiny is not available - visualization apps will not be mounted")
+
+# ... rest of existing code ...
 
 # Set up templates
 templates_path = Path(__file__).parent.parent / "templates"

webapp/app/shiny_apps/heatmap_app.py

@@ -76,8 +76,13 @@ def filter_to_icon_url(filter_name: str) -> str:
     return f"/static/filters/{filter_name}.png"
 
 
-def create_app(api_base_url: str = "http://localhost:8000"):
-    """Create the PyShiny heatmap app."""
+def create_app(api_base_url: str = "http://localhost:8000", fastapi_app=None):
+    """Create the PyShiny heatmap app.
+    
+    Args:
+        api_base_url: Base URL for API requests (used if fastapi_app is None)
+        fastapi_app: Optional FastAPI app instance for internal API calls
+    """
 
     app_ui = ui.page_fluid(
         ui.head_content(
@@ -137,24 +142,19 @@ def create_app(api_base_url: str = "http://localhost:8000"):
                 window.addEventListener('message', function(event) {{
                     if (event.data && event.data.type === 'setParams') {{
                         console.log('[Heatmap] Received params via postMessage:', event.data);
-<<<<<<< HEAD
-                        setShinyParams(event.data.job_id, event.data.batch_index);
-                    }}
-=======
                         // Wait for Shiny to be ready, then set input values
-                        if (typeof Shiny !== 'undefined' && Shiny.setInputValue) {
+                        if (typeof Shiny !== 'undefined' && Shiny.setInputValue) {{
                             Shiny.setInputValue('pm_job_id', event.data.job_id);
                             Shiny.setInputValue('pm_batch_index', event.data.batch_index);
-                        } else {
+                        }} else {{
                            
                             // Retry after Shiny loads
-                            document.addEventListener('shiny:connected', function() {
+                            document.addEventListener('shiny:connected', function() {{
                                 Shiny.setInputValue('pm_job_id', event.data.job_id);
                                 Shiny.setInputValue('pm_batch_index', event.data.batch_index);
-                            });
-                        }
-                    }
->>>>>>> feat/remove-checkboxes
+                            }});
+                        }}
+                    }}
                     // Handle download request from parent
                     if (event.data && event.data.type === 'downloadRequest') {{
                         console.log('[Heatmap] Download requested');
@@ -204,7 +204,7 @@ def create_app(api_base_url: str = "http://localhost:8000"):
                     setTimeout(retrySetParams, 1000);
                 }});
             """),
-            ui.tags.style("""
+        ui.tags.style("""
                 body {
                     font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, sans-serif;
                     background: #f9fafb;
@@ -236,7 +236,7 @@ def create_app(api_base_url: str = "http://localhost:8000"):
                 }
             """)
         ),
-        ui.row(
+    ui.row(
             ui.column(
                 12,
                 ui.div(
@@ -274,29 +274,42 @@ def create_app(api_base_url: str = "http://localhost:8000"):
             print(f"[Heatmap Server] params_received set to True", flush=True)
 
             try:
-                url = f"{api_base_url}/api/vis_data/{job_id}"
-                
-                if batch_index is not None:
-                    url += f"?batch_index={batch_index}"
-
-                print(f"[Heatmap Server] Making API request to: {url}", flush=True)
-
-                async with httpx.AsyncClient(timeout=60.0) as client:
-                    print(f"[Heatmap] GET {url}", flush=True)
-                    response = await client.get(url)
+                # Try to use internal FastAPI app if available, otherwise use HTTP
+                if fastapi_app is not None:
+                    # Use TestClient for internal requests (synchronous but works)
+                    from fastapi.testclient import TestClient
+                    client = TestClient(fastapi_app)
+                    url_path = f"/api/vis_data/{job_id}"
+                    if batch_index is not None:
+                        url_path += f"?batch_index={batch_index}"
+                    print(f"[Heatmap Server] Making internal API request to: {url_path}", flush=True)
+                    response = client.get(url_path)
                     print(f"[Heatmap Server] API response status: {response.status_code}", flush=True)
-                    response.raise_for_status()
+                    if response.status_code != 200:
+                        raise Exception(f"API returned status {response.status_code}: {response.text}")
                     data = response.json()
-                    print(f"[Heatmap Server] API response data keys: {list(data.keys()) if data else 'None'}", flush=True)
-                    vis_data.set(data)
-                    error_message.set(None)  # Clear any error
-                    print("[Heatmap Server] vis_data set successfully", flush=True)
-            except httpx.HTTPError as e:
-                error_msg = f"HTTP Error fetching data: {str(e)}"
-                print(f"[Heatmap Server] {error_msg}", flush=True)
-                error_message.set(error_msg)
+                else:
+                    # Fallback to HTTP request
+                    url = f"{api_base_url}/api/vis_data/{job_id}"
+                    if batch_index is not None:
+                        url += f"?batch_index={batch_index}"
+                    print(f"[Heatmap Server] Making HTTP API request to: {url}", flush=True)
+                    async with httpx.AsyncClient(
+                        timeout=60.0,
+                        follow_redirects=True,
+                        verify=False
+                    ) as client:
+                        response = await client.get(url)
+                        print(f"[Heatmap Server] API response status: {response.status_code}", flush=True)
+                        response.raise_for_status()
+                        data = response.json()
+                
+                print(f"[Heatmap Server] API response data keys: {list(data.keys()) if data else 'None'}", flush=True)
+                vis_data.set(data)
+                error_message.set(None)  # Clear any error
+                print("[Heatmap Server] vis_data set successfully", flush=True)
             except Exception as e:
-                error_msg = f"Unexpected error: {type(e).__name__}: {str(e)}"
+                error_msg = f"Error fetching data: {type(e).__name__}: {str(e)}"
                 print(f"[Heatmap Server] {error_msg}", flush=True)
                 import traceback
                 traceback.print_exc()
@@ -375,7 +388,7 @@ def create_app(api_base_url: str = "http://localhost:8000"):
             )
 
             # Highlight exon region
-            fig.add_vrect(x0=start-0.5, x1=end-0.5, fillcolor="#d0d0d0", line_width=0, opacity=0.1)
+            #fig.add_vrect(x0=start-0.5, x1=end-0.5, fillcolor="#d0d0d0", line_width=0, opacity=0.1)
 
             # Add filter icons to the left of y-axis labels
             fig.update_layout(images=[])
@@ -427,17 +440,17 @@ def create_app(api_base_url: str = "http://localhost:8000"):
                     "toImageButtonOptions": {
                         "format": "svg",
                         "filename": "heatmap_view",
-<<<<<<< HEAD
-                        "height": 700,
-                        "width": 1200,
-=======
                         "height": 500,
                         "width": 1100,
                         "scale": 2
->>>>>>> feat/remove-checkboxes
                     },
                     "displayModeBar": True,
-                    "modeBarButtonsToAdd": ["toImage"],
+                    
+                    "modeBarButtons": [[
+                        "zoom2d",
+                        "toImage"
+                    ]],
+                    "displaylogo": False,
                 },
             )
 
@@ -447,4 +460,4 @@ def create_app(api_base_url: str = "http://localhost:8000"):
 
 
 # Create the app instance
-app = create_app()
+#app = create_app()

webapp/app/shiny_apps/silhouette_app.py

@@ -84,8 +84,13 @@ def position_totals_for_selected_filters(nucleotide_activations_children, L, sel
     return side_to_total(incl_node), side_to_total(skip_node)
 
 
-def create_app(api_base_url: str = "http://localhost:8000"):
-    """Create the PyShiny silhouette app."""
+def create_app(api_base_url: str = "http://localhost:8000", fastapi_app=None):
+    """Create the PyShiny silhouette app.
+    
+    Args:
+        api_base_url: Base URL for API requests (used if fastapi_app is None)
+        fastapi_app: Optional FastAPI app instance for internal API calls
+    """
 
     app_ui = ui.page_fluid(
         ui.head_content(
@@ -273,27 +278,42 @@ def create_app(api_base_url: str = "http://localhost:8000"):
             print(f"[Silhouette Server] params_received set to True", flush=True)
 
             try:
-                url = f"{api_base_url}/api/vis_data/{job_id}"
-                if batch_index is not None:
-                    url += f"?batch_index={batch_index}"
-
-                print(f"[Silhouette Server] Making API request to: {url}", flush=True)
-
-                async with httpx.AsyncClient(timeout=60.0) as client:
-                    response = await client.get(url)
+                # Try to use internal FastAPI app if available, otherwise use HTTP
+                if fastapi_app is not None:
+                    # Use TestClient for internal requests (synchronous but works)
+                    from fastapi.testclient import TestClient
+                    client = TestClient(fastapi_app)
+                    url_path = f"/api/vis_data/{job_id}"
+                    if batch_index is not None:
+                        url_path += f"?batch_index={batch_index}"
+                    print(f"[Silhouette Server] Making internal API request to: {url_path}", flush=True)
+                    response = client.get(url_path)
                     print(f"[Silhouette Server] API response status: {response.status_code}", flush=True)
-                    response.raise_for_status()
+                    if response.status_code != 200:
+                        raise Exception(f"API returned status {response.status_code}: {response.text}")
                     data = response.json()
-                    print(f"[Silhouette Server] API response data keys: {list(data.keys()) if data else 'None'}", flush=True)
-                    vis_data.set(data)
-                    error_message.set(None)  # Clear any error
-                    print("[Silhouette Server] vis_data set successfully", flush=True)
-            except httpx.HTTPError as e:
-                error_msg = f"HTTP Error fetching data: {str(e)}"
-                print(f"[Silhouette Server] {error_msg}", flush=True)
-                error_message.set(error_msg)
+                else:
+                    # Fallback to HTTP request
+                    url = f"{api_base_url}/api/vis_data/{job_id}"
+                    if batch_index is not None:
+                        url += f"?batch_index={batch_index}"
+                    print(f"[Silhouette Server] Making HTTP API request to: {url}", flush=True)
+                    async with httpx.AsyncClient(
+                        timeout=60.0,
+                        follow_redirects=True,
+                        verify=False
+                    ) as client:
+                        response = await client.get(url)
+                        print(f"[Silhouette Server] API response status: {response.status_code}", flush=True)
+                        response.raise_for_status()
+                        data = response.json()
+                
+                print(f"[Silhouette Server] API response data keys: {list(data.keys()) if data else 'None'}", flush=True)
+                vis_data.set(data)
+                error_message.set(None)  # Clear any error
+                print("[Silhouette Server] vis_data set successfully", flush=True)
             except Exception as e:
-                error_msg = f"Unexpected error: {type(e).__name__}: {str(e)}"
+                error_msg = f"Error fetching data: {type(e).__name__}: {str(e)}"
                 print(f"[Silhouette Server] {error_msg}", flush=True)
                 import traceback
                 traceback.print_exc()
@@ -352,7 +372,7 @@ def create_app(api_base_url: str = "http://localhost:8000"):
             ax.bar(x, -skip_total, width=1, color="#f0a5a5", label="Skipping")
 
             # Shade exon region
-            ax.axvspan(start - 0.5, end - 0.5, color="#d0d0d0", alpha=0.15)
+            #ax.axvspan(start - 0.5, end - 0.5, color="#d0d0d0", alpha=0.15)
             ax.axhline(0, linewidth=1, color='black')
 
             ax.set_xticks(x)
@@ -402,4 +422,4 @@ def create_app(api_base_url: str = "http://localhost:8000"):
 
 
 # Create the app instance
-app = create_app()
+#app = create_app()

webapp/templates/base.html

@@ -110,65 +110,6 @@
                             </div>
                         </div>
 
-                        <!-- Auth dropdown -->
-                        <div id="auth-nav-desktop" class="relative">
-                            <!-- Not logged in: show Login button -->
-                            <div id="auth-logged-out">
-                                <button onclick="toggleAuthDropdown()" class="px-3 py-2 text-sm font-medium text-gray-700 hover:text-primary-600 hover:bg-gray-50 rounded-md flex items-center">
-                                    Login
-                                    <svg class="ml-1 h-4 w-4" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                                        <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M19 9l-7 7-7-7" />
-                                    </svg>
-                                </button>
-                                <!-- Dropdown menu -->
-                                <div id="auth-dropdown" class="hidden absolute right-0 mt-2 w-72 bg-white rounded-lg shadow-lg border border-gray-200 p-4 z-50">
-                                    <!-- Message area -->
-                                    <div id="auth-message" class="hidden mb-3 p-3 rounded-md text-sm"></div>
-
-                                    <!-- Form -->
-                                    <div id="auth-form-container">
-                                        <div class="space-y-3">
-                                            <div>
-                                                <label for="auth-email" class="block text-xs font-medium text-gray-700 mb-1">Email</label>
-                                                <input type="email" id="auth-email" placeholder="user@example.com"
-                                                    class="w-full px-3 py-2 border border-gray-300 rounded-md text-sm focus:outline-none focus:ring-2 focus:ring-primary-500 focus:border-primary-500">
-                                            </div>
-                                            <div>
-                                                <label for="auth-password" class="block text-xs font-medium text-gray-700 mb-1">Password</label>
-                                                <input type="password" id="auth-password" placeholder="••••••••"
-                                                    class="w-full px-3 py-2 border border-gray-300 rounded-md text-sm focus:outline-none focus:ring-2 focus:ring-primary-500 focus:border-primary-500">
-                                            </div>
-                                            <button onclick="submitAuth()" id="auth-submit-btn"
-                                                class="w-full py-2 px-4 bg-primary-600 text-white text-sm font-medium rounded-md hover:bg-primary-700 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-primary-500 disabled:opacity-50 disabled:cursor-not-allowed flex items-center justify-center">
-                                                <span id="auth-btn-text">Continue</span>
-                                                <svg id="auth-loading" class="hidden animate-spin ml-2 h-4 w-4 text-white" fill="none" viewBox="0 0 24 24">
-                                                    <circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle>
-                                                    <path class="opacity-75" fill="currentColor" d="M4 12a8 8 0 018-8V0C5.373 0 0 5.373 0 12h4zm2 5.291A7.962 7.962 0 014 12H0c0 3.042 1.135 5.824 3 7.938l3-2.647z"></path>
-                                                </svg>
-                                            </button>
-                                        </div>
-                                        <div class="mt-3 pt-3 border-t border-gray-200">
-                                            <p class="text-xs text-gray-500 text-center">No account? We'll create one automatically.</p>
-                                        </div>
-                                    </div>
-                                </div>
-                            </div>
-
-                            <!-- Logged in: show email + logout dropdown -->
-                            <div id="auth-logged-in" class="hidden">
-                                <button onclick="toggleUserDropdown()" class="px-3 py-2 text-sm font-medium text-gray-700 hover:text-primary-600 hover:bg-gray-50 rounded-md flex items-center">
-                                    <span id="user-email-display" class="max-w-[150px] truncate"></span>
-                                    <svg class="ml-1 h-4 w-4" fill="none" viewBox="0 0 24 24" stroke="currentColor">
-                                        <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M19 9l-7 7-7-7" />
-                                    </svg>
-                                </button>
-                                <div id="user-dropdown" class="hidden absolute right-0 mt-2 w-48 bg-white rounded-lg shadow-lg border border-gray-200 py-1 z-50">
-                                    <button onclick="logoutUser()" class="w-full text-left px-4 py-2 text-sm text-gray-700 hover:bg-gray-100">
-                                        Logout
-                                    </button>
-                                </div>
-                            </div>
-                        </div>
                     </div>
 
                     <!-- Mobile menu button -->
@@ -223,29 +164,6 @@
                         </div>
                     </div>
 
-                    <!-- Auth links mobile -->
-                    <div id="auth-nav-mobile" class="border-t border-gray-200 pt-2 mt-2">
-                        <div id="mobile-auth-logged-out">
-                            <button onclick="toggleMobileAuthForm()" class="w-full text-left px-3 py-2 text-base font-medium text-gray-700 hover:text-primary-600 hover:bg-gray-50 rounded-md">Login</button>
-                            <!-- Mobile auth form -->
-                            <div id="mobile-auth-form" class="hidden px-3 py-2 space-y-3">
-                                <div id="mobile-auth-message" class="hidden p-3 rounded-md text-sm"></div>
-                                <input type="email" id="mobile-auth-email" placeholder="Email"
-                                    class="w-full px-3 py-2 border border-gray-300 rounded-md text-sm">
-                                <input type="password" id="mobile-auth-password" placeholder="Password"
-                                    class="w-full px-3 py-2 border border-gray-300 rounded-md text-sm">
-                                <button onclick="submitMobileAuth()" id="mobile-auth-submit"
-                                    class="w-full py-2 px-4 bg-primary-600 text-white text-sm font-medium rounded-md hover:bg-primary-700">
-                                    Continue
-                                </button>
-                                <p class="text-xs text-gray-500 text-center">No account? We'll create one automatically.</p>
-                            </div>
-                        </div>
-                        <div id="mobile-auth-logged-in" class="hidden">
-                            <div class="px-3 py-2 text-sm text-gray-600" id="mobile-user-email"></div>
-                            <button onclick="logoutUser()" class="w-full text-left px-3 py-2 text-base font-medium text-gray-700 hover:text-primary-600 hover:bg-gray-50 rounded-md">Logout</button>
-                        </div>
-                    </div>
                 </div>
             </div>
         </nav>

webapp/templates/result.html

@@ -129,9 +129,7 @@
                         </svg>
                     </div>
                     <div class="collapsible-content">
-                        <p class="text-sm text-gray-500 mb-4">
-                            Blue = inclusion strength, red = skipping strength per position.
-                        </p>
+                        
                         <div id="silhouette-container" class="w-full" style="min-height: 488px;">
                             <iframe
                                 id="silhouette-iframe"
@@ -153,9 +151,7 @@
                         </svg>
                     </div>
                     <div class="collapsible-content">
-                        <p class="text-sm text-gray-500 mb-4">
-                            Blue = inclusion, red = skipping, with filter icons.
-                        </p>
+                        
                         <div id="heatmap-container" class="w-full" style="min-height: 675px;">
                             <iframe
                                 id="heatmap-iframe"