patholens 2.0.2__tar.gz → 2.0.4__tar.gz

patholens-2.0.4/PKG-INFO

@@ -0,0 +1,88 @@
+Metadata-Version: 2.4
+Name: patholens
+Version: 2.0.4
+Summary: A command-line tool to manage, deploy, and launch PathoLens with Google Colab or local backends.
+Requires-Python: >=3.13
+Requires-Dist: click>=8.0.0
+Requires-Dist: fastapi>=0.110.0
+Requires-Dist: google-colab-cli>=0.1.0
+Requires-Dist: httpx>=0.24.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: openslide-bin>=4.0.1.1
+Requires-Dist: openslide-python>=1.3.0
+Requires-Dist: pillow>=10.0.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pyjwt[crypto]>=2.8.0
+Requires-Dist: python-multipart>=0.0.9
+Requires-Dist: sqlalchemy>=2.0.0
+Requires-Dist: uvicorn[standard]>=0.20.0
+Requires-Dist: websockets>=12.0
+Description-Content-Type: text/markdown
+
+# 🔬 PathoLens Digital Pathology Workstation
+
+PathoLens is a digital pathology workstation & AI workspace with a command-line launcher supporting **Local Machine** and **Google Colab Cloud VM** execution backends.
+
+---
+
+## 🚀 Key Features
+
+*   **Dual Deployment Target:** Run completely locally on your hardware, or spin up a free Google Colab GPU-accelerated cloud VM with one command.
+*   **Zero-friction Colab Deploy (Zero Code Uploads):** The CLI uses PyPI directly. Instead of slow zip uploads of the codebase, it initiates a PyPI installation (`uv pip install`) over Google's datacenter backbone (under 5 seconds) and only uploads the locally compiled static Next.js frontend (~6MB `static.zip`).
+*   **Dynamic Slide Directory Configuration:** Switch slide folders dynamically inside the browser UI Settings modal without having to restart the backend. Point it to local directories (e.g. `/home/prime/slides`) or Google Drive paths (`/content/drive/MyDrive/...`).
+*   **Edge AI Diagnostics:** Supports local execution of the `gemma-4-E2B-it-litert-lm` LiteRT model for local digital pathology clinical questions and diagnostics.
+
+---
+
+## 📦 Installation
+
+To install the CLI globally using `uv`:
+
+```bash
+uv tool install patholens
+```
+
+---
+
+## 🛠️ Usage
+
+Simply run:
+
+```bash
+patholens launch
+```
+
+This launches the onboarding wizard in your terminal:
+
+```
+ █▀█ █▀█ ▀█▀ █▄█ █▀█ █   █▀▀ █▄ █ █▀
+ █▀▀ █▀█  █  █ █ █▄█ █▄▄ ██▄ █ ▀█ ▄█ cli v2.0.2
+ 🔬 Digital Pathology Workstation & AI Workspace
+
+ }  Environment: Cloud-Scalable / Multi-Tenant Ready
+ }  Local Fallback: SQLite + Local Slide Storage
+
+? Where would you like to run the PathoLens backend?
+  1) Local Machine (Your computer's CPU/GPU)
+  2) Google Colab VM (Free cloud CPU/GPU accelerators)
+```
+
+### Option 1: Local Machine
+Runs a local FastAPI backend and serves the Next.js frontend statically.
+*   **Local AI option:** You can choose to download the `litert_lm` package and cache the `gemma-4-E2B-it-litert-lm` model for local inference.
+*   **Launch link:** The CLI automatically opens your default browser at `http://localhost:8000`.
+
+### Option 2: Google Colab VM
+*   **Drive Integration:** Prompts you to mount your Google Drive on the VM.
+*   **Fast Setup:** Installs `patholens` from PyPI, uploads and extracts the frontend `static.zip`, installs slide bindings (`libopenslide0`), and opens a Cloudflare secure tunnel.
+*   **Direct Browser Launch:** The CLI automatically grabs the public `*.trycloudflare.com` tunnel URL and opens it in your web browser.
+
+---
+
+## ⚙️ Slide Directory Configuration
+
+You can configure the active slide folder inside the browser UI dashboard.
+1.  Click the **Settings** gear icon in the header.
+2.  Input the absolute path to your slide directory (e.g. `/content/drive/MyDrive/Slides` on Colab, or a local directory).
+3.  Click **Save Settings**. The backend updates its active path on the fly and immediately lists the `.svs` files found in the folder.
+

patholens-2.0.4/README.md

@@ -0,0 +1,67 @@
+# 🔬 PathoLens Digital Pathology Workstation
+
+PathoLens is a digital pathology workstation & AI workspace with a command-line launcher supporting **Local Machine** and **Google Colab Cloud VM** execution backends.
+
+---
+
+## 🚀 Key Features
+
+*   **Dual Deployment Target:** Run completely locally on your hardware, or spin up a free Google Colab GPU-accelerated cloud VM with one command.
+*   **Zero-friction Colab Deploy (Zero Code Uploads):** The CLI uses PyPI directly. Instead of slow zip uploads of the codebase, it initiates a PyPI installation (`uv pip install`) over Google's datacenter backbone (under 5 seconds) and only uploads the locally compiled static Next.js frontend (~6MB `static.zip`).
+*   **Dynamic Slide Directory Configuration:** Switch slide folders dynamically inside the browser UI Settings modal without having to restart the backend. Point it to local directories (e.g. `/home/prime/slides`) or Google Drive paths (`/content/drive/MyDrive/...`).
+*   **Edge AI Diagnostics:** Supports local execution of the `gemma-4-E2B-it-litert-lm` LiteRT model for local digital pathology clinical questions and diagnostics.
+
+---
+
+## 📦 Installation
+
+To install the CLI globally using `uv`:
+
+```bash
+uv tool install patholens
+```
+
+---
+
+## 🛠️ Usage
+
+Simply run:
+
+```bash
+patholens launch
+```
+
+This launches the onboarding wizard in your terminal:
+
+```
+ █▀█ █▀█ ▀█▀ █▄█ █▀█ █   █▀▀ █▄ █ █▀
+ █▀▀ █▀█  █  █ █ █▄█ █▄▄ ██▄ █ ▀█ ▄█ cli v2.0.2
+ 🔬 Digital Pathology Workstation & AI Workspace
+
+ }  Environment: Cloud-Scalable / Multi-Tenant Ready
+ }  Local Fallback: SQLite + Local Slide Storage
+
+? Where would you like to run the PathoLens backend?
+  1) Local Machine (Your computer's CPU/GPU)
+  2) Google Colab VM (Free cloud CPU/GPU accelerators)
+```
+
+### Option 1: Local Machine
+Runs a local FastAPI backend and serves the Next.js frontend statically.
+*   **Local AI option:** You can choose to download the `litert_lm` package and cache the `gemma-4-E2B-it-litert-lm` model for local inference.
+*   **Launch link:** The CLI automatically opens your default browser at `http://localhost:8000`.
+
+### Option 2: Google Colab VM
+*   **Drive Integration:** Prompts you to mount your Google Drive on the VM.
+*   **Fast Setup:** Installs `patholens` from PyPI, uploads and extracts the frontend `static.zip`, installs slide bindings (`libopenslide0`), and opens a Cloudflare secure tunnel.
+*   **Direct Browser Launch:** The CLI automatically grabs the public `*.trycloudflare.com` tunnel URL and opens it in your web browser.
+
+---
+
+## ⚙️ Slide Directory Configuration
+
+You can configure the active slide folder inside the browser UI dashboard.
+1.  Click the **Settings** gear icon in the header.
+2.  Input the absolute path to your slide directory (e.g. `/content/drive/MyDrive/Slides` on Colab, or a local directory).
+3.  Click **Save Settings**. The backend updates its active path on the fly and immediately lists the `.svs` files found in the folder.
+

{patholens-2.0.2 → patholens-2.0.4}/patholens-backend/app/main.py

@@ -468,6 +468,34 @@ async def get_toxicity(current_user: dict = Depends(get_current_user)):
         }
     ]
 
+class SlidePathRequest(pydantic.BaseModel):
+    path: str
+
+@app.post("/api/settings/slide_path")
+async def update_slide_path(request: SlidePathRequest, current_user: dict = Depends(get_current_user)):
+    global SLIDE_DIR
+    target_path = os.path.abspath(request.path)
+    if not os.path.exists(target_path):
+        raise HTTPException(status_code=400, detail=f"Directory path does not exist: {target_path}")
+    
+    SLIDE_DIR = target_path
+    logger.info("Slide directory dynamically changed to: %s", SLIDE_DIR)
+    
+    # Return updated slide list
+    slides = []
+    if os.path.exists(SLIDE_DIR):
+        slides = [f for f in os.listdir(SLIDE_DIR) if f.endswith('.svs')]
+    return {
+        "status": "success",
+        "slide_dir": SLIDE_DIR,
+        "slides": slides
+    }
+
+@app.get("/api/settings/slide_path")
+async def get_slide_path(current_user: dict = Depends(get_current_user)):
+    return {"slide_dir": SLIDE_DIR}
+
+
 class OncoLLMQuery(pydantic.BaseModel):
     query: str
     context: Optional[dict] = None
@@ -534,8 +562,11 @@ async def serve_frontend(full_path: str):
     if os.path.isfile(candidate):
         return FileResponse(candidate)
 
+    html_candidate = os.path.join(STATIC_FRONTEND_DIR, f"{full_path}.html")
+    if full_path and os.path.isfile(html_candidate):
+        return FileResponse(html_candidate)
+
     if STATIC_INDEX and os.path.isfile(STATIC_INDEX):
         return FileResponse(STATIC_INDEX)
 
     raise HTTPException(status_code=404, detail="Not Found")
-

{patholens-2.0.2 → patholens-2.0.4}/patholens-ui/app/dashboard/page.tsx

@@ -1,7 +1,7 @@
 'use client';
 
 import React, { useEffect, useState } from 'react';
-import { Search, AlertCircle, RefreshCw, Clock, FileText, CheckCircle, LogOut } from 'lucide-react';
+import { Search, AlertCircle, RefreshCw, Clock, FileText, CheckCircle, LogOut, Settings } from 'lucide-react';
 import Link from 'next/link';
 import { useRouter } from 'next/navigation';
 import Image from 'next/image';
@@ -14,6 +14,53 @@ export default function Dashboard() {
     const [loading, setLoading] = useState(true);
     const [error, setError] = useState<string | null>(null);
 
+    // Dynamic Slide Storage Configuration
+    const [isSettingsOpen, setIsSettingsOpen] = useState(false);
+    const [newSlidePath, setNewSlidePath] = useState('');
+    const [currentSlidePath, setCurrentSlidePath] = useState('');
+
+    const fetchSettings = async () => {
+        try {
+            const res = await fetch(`${config.apiBaseUrl}/api/settings/slide_path`, {
+                headers: {
+                    'Authorization': `Bearer ${authHelper.getToken()}`
+                }
+            });
+            if (res.ok) {
+                const data = await res.json();
+                setCurrentSlidePath(data.slide_dir);
+                setNewSlidePath(data.slide_dir);
+            }
+        } catch (err) {
+            console.error("Failed to fetch settings:", err);
+        }
+    };
+
+    const saveSlidePath = async () => {
+        try {
+            const res = await fetch(`${config.apiBaseUrl}/api/settings/slide_path`, {
+                method: 'POST',
+                headers: {
+                    'Content-Type': 'application/json',
+                    'Authorization': `Bearer ${authHelper.getToken()}`
+                },
+                body: JSON.stringify({ path: newSlidePath })
+            });
+            if (res.ok) {
+                const data = await res.json();
+                setCurrentSlidePath(data.slide_dir);
+                setIsSettingsOpen(false);
+                fetchSlides();
+            } else {
+                const errData = await res.json();
+                alert(`Error: ${errData.detail || 'Failed to update slide path'}`);
+            }
+        } catch (err) {
+            console.error("Failed to save slide path:", err);
+            alert("Connection error. Could not save settings.");
+        }
+    };
+
     const handleLogout = () => {
         authHelper.clearToken();
         router.push('/login');
@@ -41,6 +88,7 @@ export default function Dashboard() {
 
     useEffect(() => {
         fetchSlides();
+        fetchSettings();
     }, []);
 
     // Mock data for patient insights
@@ -92,6 +140,13 @@ export default function Dashboard() {
                         <div className="w-10 h-10 bg-purple-600 rounded-full flex items-center justify-center text-white font-bold">
                             SC
                         </div>
+                        <button
+                            onClick={() => setIsSettingsOpen(true)}
+                            className="p-2 text-gray-400 hover:text-blue-600 transition-colors"
+                            title="Slide Folder Settings"
+                        >
+                            <Settings size={20} />
+                        </button>
                         <button
                             onClick={handleLogout}
                             className="p-2 text-gray-400 hover:text-red-600 transition-colors"
@@ -240,6 +295,66 @@ export default function Dashboard() {
                     </div>
                 )}
             </div>
+
+            {/* Slide Directory Settings Modal */}
+            {isSettingsOpen && (
+                <div className="fixed inset-0 bg-black/60 backdrop-blur-sm z-50 flex items-center justify-center p-4">
+                    <div className="bg-white rounded-2xl border border-gray-200 shadow-2xl w-full max-w-md overflow-hidden text-gray-900">
+                        <div className="p-6 border-b border-gray-100 flex items-center justify-between bg-gray-50">
+                            <h3 className="font-bold text-gray-800 flex items-center gap-2">
+                                <Settings size={18} className="text-blue-600" />
+                                Slide Storage Configuration
+                            </h3>
+                            <button 
+                                onClick={() => setIsSettingsOpen(false)}
+                                className="text-gray-400 hover:text-gray-600 text-sm font-semibold"
+                            >
+                                Close
+                            </button>
+                        </div>
+                        <div className="p-6 space-y-4">
+                            <div>
+                                <label className="block text-xs font-bold text-gray-500 uppercase tracking-wider mb-2">
+                                    Current Slides Folder
+                                </label>
+                                <div className="bg-gray-50 p-3 rounded-lg border border-gray-100 font-mono text-xs text-gray-700 select-all truncate" title={currentSlidePath}>
+                                    {currentSlidePath || 'Not configured'}
+                                </div>
+                            </div>
+                            <div>
+                                <label className="block text-xs font-bold text-gray-500 uppercase tracking-wider mb-2">
+                                    New Slide Directory Path
+                                </label>
+                                <input
+                                    type="text"
+                                    value={newSlidePath}
+                                    onChange={(e) => setNewSlidePath(e.target.value)}
+                                    placeholder="e.g. /home/prime/data/slides"
+                                    className="w-full px-3 py-2 border border-gray-200 rounded-xl focus:outline-none focus:ring-2 focus:ring-blue-500 font-mono text-sm text-gray-900 bg-white"
+                                />
+                                <p className="text-[10px] text-gray-400 mt-1.5 leading-relaxed">
+                                    Enter the absolute directory path on the server/VM where SVS slides are located.
+                                    For Colab sessions, this is typically under <code className="bg-gray-100 px-1 py-0.5 rounded text-blue-600 font-mono">/content/drive/MyDrive/...</code>
+                                </p>
+                            </div>
+                        </div>
+                        <div className="p-4 border-t border-gray-100 bg-gray-50 flex justify-end gap-2">
+                            <button
+                                onClick={() => setIsSettingsOpen(false)}
+                                className="px-4 py-2 border border-gray-200 rounded-lg text-sm text-gray-600 hover:bg-gray-100 bg-white"
+                            >
+                                Cancel
+                            </button>
+                            <button
+                                onClick={saveSlidePath}
+                                className="px-4 py-2 bg-blue-600 hover:bg-blue-700 text-white rounded-lg text-sm font-semibold shadow-sm"
+                            >
+                                Save Settings
+                            </button>
+                        </div>
+                    </div>
+                </div>
+            )}
         </div>
     );
 }

{patholens-2.0.2 → patholens-2.0.4}/patholens_cli/__init__.py

@@ -1,2 +1,2 @@
 # PathoLens CLI module
-__version__ = "2.0.2"
+__version__ = "2.0.4"

{patholens-2.0.2 → patholens-2.0.4}/patholens_cli/main.py

@@ -18,7 +18,7 @@ CONFIG_PATH = os.path.join(CONFIG_DIR, "config.json")
 
 BANNER = """\033[95m
  █▀█ █▀█ ▀█▀ █▄█ █▀█ █   █▀▀ █▄ █ █▀
- █▀▀ █▀█  █  █ █ █▄█ █▄▄ ██▄ █ ▀█ ▄█\033[0m \033[93mcli v2.0.2\033[0m
+ █▀▀ █▀█  █  █ █ █▄█ █▄▄ ██▄ █ ▀█ ▄█\033[0m \033[93mcli v2.0.4\033[0m
  \033[90m🔬 Digital Pathology Workstation & AI Workspace\033[0m
 """
 
@@ -272,7 +272,8 @@ def launch(colab, gpu, session, local, litert_model, litert_backend):
                 port=8000, 
                 static_dir=os.path.join(project_root, "patholens-ui", "out"), 
                 litert_model=litert_model, 
-                litert_backend=litert_backend or "cpu"
+                litert_backend=litert_backend or "cpu",
+                sample_data_path=None
             )
         except KeyboardInterrupt:
             click.echo("\n[patholens] Local server stopped.")
@@ -336,12 +337,8 @@ def launch(colab, gpu, session, local, litert_model, litert_backend):
         click.echo("[patholens] Aborting launch: Frontend static export files missing.")
         return
 
-    # Create temporary zip archive of whole project and static frontend
+    # Create temporary zip archive of static frontend
     with tempfile.TemporaryDirectory() as temp_dir:
-        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)
-        
         click.echo("[patholens] Packaging static UI files...")
         ui_zip = os.path.join(temp_dir, "static.zip")
         zip_dir(os.path.join(project_root, "patholens-ui", "out"), ui_zip)
@@ -362,9 +359,6 @@ def launch(colab, gpu, session, local, litert_model, litert_backend):
         time.sleep(10)
 
         # Upload files
-        click.echo("[patholens] Uploading project codebase...")
-        subprocess.run(["colab", "upload", "-s", session, project_zip, "content/patholens.zip"], check=True)
-        
         click.echo("[patholens] Uploading static UI bundle...")
         subprocess.run(["colab", "upload", "-s", session, ui_zip, "content/static.zip"], check=True)
 
@@ -383,9 +377,6 @@ import subprocess
 import time
 
 print("[colab-setup] Extracting files...")
-with zipfile.ZipFile('/content/patholens.zip', 'r') as zip_ref:
-    zip_ref.extractall('/content')
-
 with zipfile.ZipFile('/content/static.zip', 'r') as zip_ref:
     zip_ref.extractall('/content/static')
 
@@ -395,8 +386,8 @@ os.system("apt-get update && apt-get install -y libopenslide0")
 print("[colab-setup] Installing uv package manager...")
 os.system("pip install uv")
 
-print("[colab-setup] Installing patholens package via uv...")
-os.system("uv pip install --system /content/patholens")
+print("[colab-setup] Installing patholens package via uv from PyPI...")
+os.system("uv pip install --system patholens")
 
 if "{litert_model or ''}":
     print("[colab-setup] Installing litert-lm package...")

{patholens-2.0.2 → patholens-2.0.4}/pyproject.toml

@@ -4,10 +4,10 @@ build-backend = "hatchling.build"
 
 [project]
 name = "patholens"
-version = "2.0.2"
+version = "2.0.4"
 description = "A command-line tool to manage, deploy, and launch PathoLens with Google Colab or local backends."
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.13"
 dependencies = [
     "click>=8.0.0",
     "fastapi>=0.110.0",

patholens-2.0.2/PKG-INFO

@@ -1,40 +0,0 @@
-Metadata-Version: 2.4
-Name: patholens
-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
-Requires-Dist: fastapi>=0.110.0
-Requires-Dist: google-colab-cli>=0.1.0
-Requires-Dist: httpx>=0.24.0
-Requires-Dist: numpy>=1.24.0
-Requires-Dist: openslide-bin>=4.0.1.1
-Requires-Dist: openslide-python>=1.3.0
-Requires-Dist: pillow>=10.0.0
-Requires-Dist: pydantic>=2.0.0
-Requires-Dist: pyjwt[crypto]>=2.8.0
-Requires-Dist: python-multipart>=0.0.9
-Requires-Dist: sqlalchemy>=2.0.0
-Requires-Dist: uvicorn[standard]>=0.20.0
-Requires-Dist: websockets>=12.0
-Description-Content-Type: text/markdown
-
-# PathoLens
-
-PathoLens is a digital pathology workstation with a CLI launcher for local or Google Colab-backed execution.
-
-## Install
-
-```bash
-uv tool install patholens
-```
-
-## Usage
-
-```bash
-patholens launch
-```
-
-The launcher can run the backend locally or package and deploy the application to a Google Colab VM. Local launch builds the bundled Next.js UI if a static export is not already present.
-
-For whole-slide image viewing, the backend uses OpenSlide.

patholens-2.0.2/README.md

@@ -1,19 +0,0 @@
-# PathoLens
-
-PathoLens is a digital pathology workstation with a CLI launcher for local or Google Colab-backed execution.
-
-## Install
-
-```bash
-uv tool install patholens
-```
-
-## Usage
-
-```bash
-patholens launch
-```
-
-The launcher can run the backend locally or package and deploy the application to a Google Colab VM. Local launch builds the bundled Next.js UI if a static export is not already present.
-
-For whole-slide image viewing, the backend uses OpenSlide.