patholens 2.0.0__tar.gz → 2.0.2__tar.gz

{patholens-2.0.0 → patholens-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: patholens
-Version: 2.0.0
+Version: 2.0.2
 Summary: A command-line tool to manage, deploy, and launch PathoLens with Google Colab or local backends.
 Requires-Python: >=3.10
 Requires-Dist: click>=8.0.0

{patholens-2.0.0 → patholens-2.0.2}/patholens-backend/app/main.py

@@ -470,7 +470,7 @@ async def get_toxicity(current_user: dict = Depends(get_current_user)):
 
 class OncoLLMQuery(pydantic.BaseModel):
     query: str
-    context: dict = {}
+    context: Optional[dict] = None
 
 @app.post("/ai/oncollm/query")
 async def query_oncollm(request: OncoLLMQuery, current_user: dict = Depends(get_current_user)):

{patholens-2.0.0 → patholens-2.0.2}/patholens-ui/app/globals.css

@@ -1,4 +1,11 @@
 @import "tailwindcss";
+@source "../components/**/*.ts";
+@source "../components/**/*.tsx";
+@source "../types.d.ts";
+@source inline("h-screen min-h-screen h-14 h-16 h-10 h-8 h-5 h-2.5 h-[40%] h-[45%] w-80 w-[400px] w-64 w-48 w-32 w-16 w-10 w-8 w-5 w-2.5 w-2 w-[40%] w-[45%] max-w-7xl max-w-md p-12 p-6 px-6 py-3.5 py-3 py-1 pr-4 pl-10 z-10 block hidden md:block sr-only");
+@source inline("top-1/2 top-4 top-[-10%] right-4 right-[-5%] bottom-[-15%] left-1/2 left-3 left-[-10%] -translate-x-1/2 -translate-y-1/2 transform gap-3 gap-8 space-y-8 divide-y divide-gray-100 border-r border-2 border-b-2 border-gray-300 border-blue-600 border-purple-600 border-red-400 border-t-white border-white/40");
+@source inline("bg-black bg-gray-400 bg-blue-50/50 bg-blue-200/30 bg-cyan-200/30 bg-purple-50/50 bg-purple-600 bg-green-500 bg-yellow-500 bg-red-500 bg-orange-500 from-gray-50 from-blue-600 via-white to-blue-50 to-indigo-600 to-cyan-500 blur-[120px] blur-[140px] drop-shadow-sm drop-shadow-md shadow-lg shadow-md shadow-blue-200 shadow-[0_0_8px_rgba(34,197,94,0.6)] shadow-[0_0_8px_rgba(234,179,8,0.6)] shadow-[0_0_8px_rgba(239,68,68,0.6)]");
+@source inline("mt-8 mt-20 mb-6 mb-8 mb-10 opacity-20 opacity-75 cursor-not-allowed font-mono text-xl text-right uppercase tracking-wider transition-all active:scale-[0.99] hover:scale-[1.01] hover:bg-blue-50 hover:bg-gray-50 hover:bg-gray-200 hover:from-blue-500 hover:from-blue-700 hover:to-cyan-400 hover:to-indigo-700 hover:text-gray-700 hover:text-red-600 hover:shadow-lg group-hover:bg-blue-200 group-hover:bg-green-200 group-hover:text-blue-700 group-hover:text-green-700 focus:ring-1 placeholder-gray-400");
 
 @theme {
   --font-sans: var(--font-geist-sans);
@@ -77,4 +84,4 @@ body {
 
 .scrollbar-thin::-webkit-scrollbar-thumb:hover {
   background-color: rgba(75, 85, 99, 0.8);
-}
+}

patholens-2.0.2/patholens-ui/next-env.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="next" />
+/// <reference types="next/image-types/global" />
+import "./.next/types/routes.d.ts";
+
+// NOTE: This file should not be edited
+// see https://nextjs.org/docs/app/api-reference/config/typescript for more information.

{patholens-2.0.0 → patholens-2.0.2}/patholens_cli/__init__.py

@@ -1,2 +1,2 @@
 # PathoLens CLI module
-__version__ = "2.0.0"
+__version__ = "2.0.2"

{patholens-2.0.0 → patholens-2.0.2}/patholens_cli/main.py

@@ -6,20 +6,45 @@ import tempfile
 import time
 import webbrowser
 import shutil
+import json
+import sys
+
+# Platform-specific import for non-blocking console input
+if sys.platform != 'win32':
+    import select
+
+CONFIG_DIR = os.path.expanduser("~/.config/patholens")
+CONFIG_PATH = os.path.join(CONFIG_DIR, "config.json")
 
 BANNER = """\033[95m
  █▀█ █▀█ ▀█▀ █▄█ █▀█ █   █▀▀ █▄ █ █▀
- █▀▀ █▀█  █  █ █ █▄█ █▄▄ ██▄ █ ▀█ ▄█\033[0m \033[93mcli v2.0.0\033[0m
+ █▀▀ █▀█  █  █ █ █▄█ █▄▄ ██▄ █ ▀█ ▄█\033[0m \033[93mcli v2.0.2\033[0m
  \033[90m🔬 Digital Pathology Workstation & AI Workspace\033[0m
 """
 
 def print_banner():
     click.echo(BANNER)
-    # Print status details similarly to the Gemini CLI screenshot
     click.echo(" \033[93m}\033[0m  \033[1mEnvironment:\033[0m Cloud-Scalable / Multi-Tenant Ready")
     click.echo(" \033[93m}\033[0m  \033[1mLocal Fallback:\033[0m SQLite + Local Slide Storage")
     click.echo()
 
+def load_config() -> dict:
+    if os.path.exists(CONFIG_PATH):
+        try:
+            with open(CONFIG_PATH, 'r') as f:
+                return json.load(f)
+        except Exception:
+            pass
+    return {}
+
+def save_config(config_data: dict):
+    try:
+        os.makedirs(CONFIG_DIR, exist_ok=True)
+        with open(CONFIG_PATH, 'w') as f:
+            json.dump(config_data, f, indent=2)
+    except Exception as e:
+        click.echo(f"[patholens] Warning: Could not save configuration: {e}")
+
 def prompt_choice(question: str, options: list) -> int:
     """Prompts the user with numbered options and returns the 1-based index selection."""
     click.echo(f"\033[96m? \033[1m{question}\033[0m")
@@ -33,10 +58,11 @@ def prompt_choice(question: str, options: list) -> int:
         click.echo(f"  \033[91mInvalid choice. Select 1-{len(options)}.\033[0m")
 
 def zip_project(src_dir: str, zip_path: str):
-    """Zips the PathoLens project directories, excluding heavy build caches and libraries."""
-    ignore_dirs = {".git", ".next", "node_modules", "out", "__pycache__", "cptac_samples", ".pytest_cache", ".gemini", "brain"}
+    """Zips the PathoLens project directories, excluding heavy build caches, local slides, and databases."""
+    ignore_dirs = {".git", ".next", "node_modules", "out", "__pycache__", "cptac_samples", "sample_data", ".pytest_cache", ".gemini", "brain"}
     with zipfile.ZipFile(zip_path, 'w', zipfile.ZIP_DEFLATED) as zipf:
         for root, dirs, files in os.walk(src_dir):
+            # Prune directories in place to prevent os.walk from scanning them
             dirs[:] = [d for d in dirs if d not in ignore_dirs]
             for file in files:
                 if file.endswith(".zip") or file.endswith(".db") or file.endswith(".svs"):
@@ -70,7 +96,7 @@ def build_frontend_locally(project_root: str) -> bool:
         
     try:
         subprocess.run(["npm", "install"], cwd=ui_dir, check=True)
-        subprocess.run(["npm", "run build"], cwd=ui_dir, check=True)
+        subprocess.run(["npm", "run", "build"], cwd=ui_dir, check=True)
         return os.path.exists(out_dir)
     except Exception as e:
         click.echo(f"[patholens] Failed to compile frontend: {e}")
@@ -80,7 +106,6 @@ def check_and_install_litert_dependencies():
     """Checks and installs local litert_lm dependencies."""
     try:
         import litert_lm
-        click.echo("[patholens] litert_lm library is already installed.")
     except ImportError:
         click.echo("[patholens] Installing litert_lm dependency locally...")
         subprocess.run(["pip", "install", "litert-lm"], check=True)
@@ -105,13 +130,16 @@ def cli():
 @click.option("--static-dir", default=None, help="Directory serving static frontend files")
 @click.option("--litert-model", default=None, help="Optional local LiteRT model path or HF repo ID")
 @click.option("--litert-backend", default="cpu", help="LiteRT backend (cpu or gpu)")
-def start_backend(port, static_dir, litert_model, litert_backend):
+@click.option("--sample-data-path", default=None, help="Directory storing SVS histopathology slides")
+def start_backend(port, static_dir, litert_model, litert_backend, sample_data_path):
     """Starts the FastAPI backend server (called on Colab or locally)."""
     if static_dir:
         os.environ["STATIC_FRONTEND_DIR"] = os.path.abspath(static_dir)
     if litert_model:
         os.environ["LITERT_MODEL_PATH"] = litert_model
         os.environ["LITERT_BACKEND"] = litert_backend
+    if sample_data_path:
+        os.environ["SAMPLE_DATA_PATH"] = os.path.abspath(sample_data_path)
 
     import uvicorn
     import sys
@@ -137,52 +165,101 @@ def launch(colab, gpu, session, local, litert_model, litert_backend):
     project_root = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
     print_banner()
 
-    # Determine launch target interactively if not provided in CLI flags
-    launch_target = None
-    if colab:
-        launch_target = "colab"
-    elif local:
-        launch_target = "local"
-    else:
-        choice = prompt_choice(
-            "Where would you like to run the PathoLens backend?",
-            ["Local Machine (Your computer's CPU/GPU)", "Google Colab VM (Free cloud CPU/GPU accelerators)"]
-        )
-        launch_target = "local" if choice == 1 else "colab"
-
-    # --- LOCAL RUN FLOW ---
-    if launch_target == "local":
-        click.echo("[patholens] Configuring Local Launch...")
+    # Try loading cached config
+    config = load_config()
+    use_saved_config = False
+    
+    if config and not (colab or local):
+        click.echo("\033[94m[patholens]\033[0m Loaded saved configuration:")
+        target_name = "Google Colab VM" if config.get("target") == "colab" else "Local Machine"
+        click.echo(f"  \033[1mTarget Environment:\033[0m {target_name}")
+        if config.get("target") == "colab":
+            click.echo(f"  \033[1mSession Name:\033[0m {config.get('session')}")
+            click.echo(f"  \033[1mGPU Option:\033[0m {config.get('gpu') or 'None'}")
+            click.echo(f"  \033[1mModel Profile:\033[0m {config.get('litert_model') or 'None'}")
+            click.echo(f"  \033[1mDrive Slides Folder:\033[0m {config.get('drive_slides_path') or 'None'}")
+        else:
+            click.echo(f"  \033[1mModel Profile:\033[0m {config.get('litert_model') or 'None'}")
+            
+        click.echo("\033[93mPress any key within 3 seconds to reconfigure...\033[0m")
         
-        # Ask about model running
-        run_model = False
-        if litert_model is None:
-            choice = prompt_choice(
-                "Would you like to run a local Gemma 4 LiteRT model for AI Diagnostics?",
-                ["Yes (Runs locally using litert_lm)", "No (Use mock diagnostics / API endpoints)"]
-            )
-            run_model = (choice == 1)
+        # Read keypress with timeout on Linux/Unix
+        if sys.platform != 'win32':
+            i, o, e = select.select([sys.stdin], [], [], 3.0)
+            if i:
+                sys.stdin.readline()  # Consume key
+                click.echo("\033[94m[patholens]\033[0m Entering reconfiguration flow...\033[0m")
+            else:
+                use_saved_config = True
+                click.echo("\033[94m[patholens]\033[0m Booting with saved configuration...\033[0m")
         else:
-            run_model = True
+            # Simple fallback timeout for other platforms
+            time.sleep(3)
+            use_saved_config = True
 
-        if run_model:
-            check_and_install_litert_dependencies()
-            if litert_model is None:
-                litert_model = "litert-community/gemma-4-E2B-it-litert-lm"
-                
+    # Parse parameters based on selections
+    launch_target = None
+    drive_slides_path = None
+    
+    if use_saved_config:
+        launch_target = config.get("target")
+        session = config.get("session")
+        gpu = config.get("gpu")
+        litert_model = config.get("litert_model")
+        litert_backend = config.get("litert_backend")
+        drive_slides_path = config.get("drive_slides_path")
+    else:
+        # Determine launch target
+        if colab:
+            launch_target = "colab"
+        elif local:
+            launch_target = "local"
+        else:
             choice = prompt_choice(
-                "Verify model artifact caching:",
-                ["Use default Hugging Face download (will download if not cached)", "Download model manually now"]
+                "Where would you like to run the PathoLens backend?",
+                ["Local Machine (Your computer's CPU/GPU)", "Google Colab VM (Free cloud CPU/GPU accelerators)"]
             )
-            if choice == 2:
-                litert_model = download_litert_model()
+            launch_target = "local" if choice == 1 else "colab"
 
-            if litert_backend is None:
+    # --- LOCAL RUN FLOW ---
+    if launch_target == "local":
+        if not use_saved_config:
+            # Ask about model running
+            run_model = False
+            if litert_model is None:
                 choice = prompt_choice(
-                    "Which hardware backend should the local model use?",
-                    ["CPU (Standard)", "GPU (Requires CUDA/MPS compatible graphics card)"]
+                    "Would you like to run a local Gemma 4 LiteRT model for AI Diagnostics?",
+                    ["Yes (Runs locally using litert_lm)", "No (Use mock diagnostics / API endpoints)"]
                 )
-                litert_backend = "gpu" if choice == 2 else "cpu"
+                run_model = (choice == 1)
+            else:
+                run_model = True
+
+            if run_model:
+                check_and_install_litert_dependencies()
+                if litert_model is None:
+                    litert_model = "litert-community/gemma-4-E2B-it-litert-lm"
+                    
+                choice = prompt_choice(
+                    "Verify model artifact caching:",
+                    ["Use default Hugging Face download (will download if not cached)", "Download model manually now"]
+                )
+                if choice == 2:
+                    litert_model = download_litert_model()
+
+                if litert_backend is None:
+                    choice = prompt_choice(
+                        "Which hardware backend should the local model use?",
+                        ["CPU (Standard)", "GPU (Requires CUDA/MPS compatible graphics card)"]
+                    )
+                    litert_backend = "gpu" if choice == 2 else "cpu"
+
+            # Save configuration
+            save_config({
+                "target": "local",
+                "litert_model": litert_model,
+                "litert_backend": litert_backend
+            })
 
         # Build UI
         build_frontend_locally(project_root)
@@ -204,33 +281,55 @@ def launch(colab, gpu, session, local, litert_model, litert_backend):
     # --- COLAB RUN FLOW ---
     click.echo("[patholens] Configuring Google Colab Launch...")
     
-    if session is None:
-        session = click.prompt("  \033[90mEnter Colab session name\033[0m", default="patholens-server")
-        
-    if gpu is None:
-        choice = prompt_choice(
-            "Which GPU accelerator would you like to request on Colab?",
-            ["None (CPU only)", "T4 GPU (Standard)", "L4 GPU (High performance)", "A100 GPU (Premium)"]
-        )
-        gpus = [None, "T4", "L4", "A100"]
-        gpu = gpus[choice - 1]
+    if not use_saved_config:
+        if session is None:
+            session = click.prompt("  \033[90mEnter Colab session name\033[0m", default="patholens-server")
+            
+        if gpu is None:
+            choice = prompt_choice(
+                "Which GPU accelerator would you like to request on Colab?",
+                ["None (CPU only)", "T4 GPU (Standard)", "L4 GPU (High performance)", "A100 GPU (Premium)"]
+            )
+            gpus = [None, "T4", "L4", "A100"]
+            gpu = gpus[choice - 1]
+
+        # Ask about model running
+        run_model_colab = False
+        if litert_model is None:
+            choice = prompt_choice(
+                "Would you like to load a LiteRT model on the Colab VM?",
+                ["Yes, load Gemma 4 E2B LiteRT (default)", "No, run backend only"]
+            )
+            run_model_colab = (choice == 1)
+        else:
+            run_model_colab = True
 
-    # Ask about model running
-    run_model_colab = False
-    if litert_model is None:
+        if run_model_colab:
+            if litert_model is None:
+                litert_model = "litert-community/gemma-4-E2B-it-litert-lm"
+            if litert_backend is None:
+                litert_backend = "gpu" if gpu else "cpu"
+
+        # Ask about slide directory on Google Drive
         choice = prompt_choice(
-            "Would you like to load a LiteRT model on the Colab VM?",
-            ["Yes, load Gemma 4 E2B LiteRT (default)", "No, run backend only"]
+            "Do you want to mount Google Drive to access your histopathology .svs slides directly?",
+            ["Yes, access slides from Google Drive", "No, use default samples on VM"]
         )
-        run_model_colab = (choice == 1)
-    else:
-        run_model_colab = True
+        if choice == 1:
+            drive_slides_path = click.prompt(
+                "  \033[90mEnter path to slides folder in Google Drive\033[0m",
+                default="/content/drive/MyDrive/PathoLens/slides"
+            )
 
-    if run_model_colab:
-        if litert_model is None:
-            litert_model = "litert-community/gemma-4-E2B-it-litert-lm"
-        if litert_backend is None:
-            litert_backend = "gpu" if gpu else "cpu"
+        # Save config
+        save_config({
+            "target": "colab",
+            "session": session,
+            "gpu": gpu,
+            "litert_model": litert_model,
+            "litert_backend": litert_backend,
+            "drive_slides_path": drive_slides_path
+        })
 
     # Build UI
     if not build_frontend_locally(project_root):
@@ -239,7 +338,7 @@ def launch(colab, gpu, session, local, litert_model, litert_backend):
 
     # Create temporary zip archive of whole project and static frontend
     with tempfile.TemporaryDirectory() as temp_dir:
-        click.echo("[patholens] Packaging codebase for Colab installation...")
+        click.echo("[patholens] Packaging codebase for Colab installation (excluding local slide directories)...")
         project_zip = os.path.join(temp_dir, "patholens.zip")
         zip_project(project_root, project_zip)
         
@@ -258,6 +357,10 @@ def launch(colab, gpu, session, local, litert_model, litert_backend):
             click.echo("[patholens] Failed to allocate Colab session VM.")
             return
 
+        # Wait 10 seconds for Colab proxy server to fully stabilize before uploading files
+        click.echo("[patholens] Waiting for Google Colab VM proxy to stabilize...")
+        time.sleep(10)
+
         # Upload files
         click.echo("[patholens] Uploading project codebase...")
         subprocess.run(["colab", "upload", "-s", session, project_zip, "content/patholens.zip"], check=True)
@@ -269,6 +372,8 @@ def launch(colab, gpu, session, local, litert_model, litert_backend):
         backend_args = "--static-dir /content/static"
         if litert_model:
             backend_args += f" --litert-model {litert_model} --litert-backend {litert_backend}"
+        if drive_slides_path:
+            backend_args += f" --sample-data-path {drive_slides_path}"
 
         # Execute VM initialization script using uv
         vm_setup_script = f"""
@@ -327,6 +432,11 @@ print("[colab-setup] Error: Failed to retrieve tunnel URL.")
         with open(setup_script_path, "w") as f:
             f.write(vm_setup_script)
 
+        # Run Drivemount if configured
+        if drive_slides_path:
+            click.echo("[patholens] Mounting Google Drive to Colab VM (accept prompts)...")
+            subprocess.run(["colab", "drivemount", "-s", session], check=True)
+
         click.echo("[patholens] Installing uv packages and tunnels on Colab...")
         exec_res = subprocess.run(["colab", "exec", "-s", session, "-f", setup_script_path], capture_output=True, text=True)
         

{patholens-2.0.0 → patholens-2.0.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "patholens"
-version = "2.0.0"
+version = "2.0.2"
 description = "A command-line tool to manage, deploy, and launch PathoLens with Google Colab or local backends."
 readme = "README.md"
 requires-python = ">=3.10"