Merge branch 'main' of github.com:bioimage-io/bioimageio-chatbot

docs/development.md

@@ -17,10 +17,13 @@ A chatbot extension object is a dictionary with the following keys:
 The following is a chatbot extension object defined in Python:
 ```python
 
+
 def get_schema():
     return {
         "my_tool": {
             "type": "object",
+            "title": "my_tool",
+            "description": "my tool",
             "properties": {
                 "my_param": {
                     "type": "number",
@@ -34,7 +37,6 @@ def my_tool(config):
     print(config["my_param"])
     return {"result": "success"}
 
-
 chatbot_extension = {
     "id": "my-extension",
     "type": "bioimageio-chatbot-extension",
@@ -59,6 +61,8 @@ const chatbotExtension = {
         return {
             my_tool: {
                 type: "object",
+                title: "my_tool",
+                description: "my tool",
                 properties: {
                     my_param: {
                         type: "number",
@@ -119,24 +123,50 @@ Below are examples demonstrating how to serve an extension with Hypha using both
 ### Serve Chatbot Extension with Hypha in JavaScript
 
 ```javascript
-const server = await api.connectToServer({server_url: "https://chat.bioimage.io"});
+const token = await login({server_url: "https://chat.bioimage.io"})
+const server = await connectToServer({server_url: "https://chat.bioimage.io", token});
 const svc = await server.registerService(chatbotExtension);
 console.log(`Extension service registered with id: ${svc.id}, you can visit the service at: https://chat.bioimage.io/public/apps/bioimageio-chatbot-client/chat?extension=${svc.id}`);
 ```
 
+**IMPORTANT: The above hypha service can only be accessed by the same user who registered the service, below you will find a section about making it public**
+
 ### Serve Chatbot Extension with Hypha in Python
 
 ```python
 from imjoy_rpc.hypha import connect_to_server, login
 
 server_url = "https://chat.bioimage.io"
-server = await connect_to_server({"server_url": server_url})
+token = await login({"server_url": server_url})
+server = await connect_to_server({"server_url": server_url, "token": token})
 svc = await server.register_service(chatbot_extension)
 print(f"Extension service registered with id: {svc.id}, you can visit the service at: {server_url}/public/apps/bioimageio-chatbot-client/chat?extension={svc.id}")
 ```
 
 After registering the extension with Hypha, you can access the chatbot with the extension by visiting the following URL: `https://chat.bioimage.io/public/apps/bioimageio-chatbot-client/chat?extension=<extension_id>`, where `<extension_id>` is the ID of the registered extension service.
 
+**IMPORTANT: The above hypha service can only be accessed by the same user who registered the service, below you will find a section about making it public**
+
+### Making Chatbot Extension Public
+
+To make it public, you need to set the visibility of the chatbot extension service to `public`.
+
+See the example below:
+
+```python
+from imjoy_rpc.hypha import connect_to_server, login
+
+server_url = "https://chat.bioimage.io"
+token = await login({"server_url": server_url})
+server = await connect_to_server({"server_url": server_url, "token": token})
+# Below, we set the visibility to public
+chatbot_extension['config'] = {"visibility": "public"}
+svc = await server.register_service(chatbot_extension)
+print(f"Extension service registered with id: {svc.id}, you can visit the service at: {server_url}/public/apps/bioimageio-chatbot-client/chat?extension={svc.id}")
+```
+
+You can also implement authorization logic in the tool function, see [hypha service authorization](https://ha.amun.ai/#/?id=service-authorization).
+
 ## Tutorial
 
 For an in-depth understanding, refer to [our detailed tutorial](./bioimage-chatbot-extension-tutorial.ipynb), accessible directly through the ImJoy Jupyter Notebook in your browser without installation. [Click here to launch the notebook](https://imjoy-notebook.netlify.app/lab/index.html?load=https://raw.githubusercontent.com/bioimage-io/bioimageio-chatbot/main/docs/bioimage-chatbot-extension-tutorial.ipynb&open=1).

knowledge-base-manifest.yaml

@@ -11,7 +11,7 @@ collections:
     format: markdown
   - name: BioImage.IO
     id: bioimage.io
-    source: https://github.com/bioimage-io/bioimage.io/archive/refs/heads/main.zip
+    source: https://github.com/bioimage-io/bioimage.io/archive/8ce3559d80f500eb34e1f75d9ea776d6efed5aef.zip
     directory: docs
     description: A platform for sharing and deploying deep learning models in bioimaging.
     base_url: https://bioimage.io/docs/
@@ -25,14 +25,14 @@ collections:
     format: markdown
   - name: bio.tools
     id: bio.tools
-    source: https://github.com/research-software-ecosystem/content/archive/refs/heads/master.zip
+    source: https://github.com/research-software-ecosystem/content/archive/954c3b2da10e951b2fbcf17825013c1c44ceddf6.zip
     directory: data
     description: A repository for research software tools with metadata.
     base_url: https://bio.tools
     format: json 
   - name: ImJoy
     id: imjoy
-    source: https://github.com/imjoy-team/ImJoy/archive/refs/heads/master.zip
+    source: https://github.com/imjoy-team/ImJoy/archive/c255d9cda9dc19d441fb7cf1eaca806e5ec71af8.zip
     directory: docs
     description: A plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools.
     base_url: https://imjoy.io/docs/#/
@@ -59,7 +59,7 @@ collections:
     format: markdown
   - name: Introduction to Bioimage Analysis
     id: book-itba
-    source: https://github.com/bioimagebook/bioimagebook.github.io/archive/refs/heads/main.zip
+    source: https://github.com/bioimagebook/bioimagebook.github.io/archive/9519fb297cece3a131718a36f642ba463c41b160.zip
     directory: chapters
     description: "A book written by Pete Bankhead about introduction to bioimage analysis, including practical exercises and Jupyter Book content"
     base_url: https://bioimagebook.github.io/
@@ -120,20 +120,19 @@ collections:
     format: pdf
   - name: ITK
     id: itk
-    source: https://github.com/InsightSoftwareConsortium/ITK/archive/refs/heads/master.zip
+    source: https://github.com/InsightSoftwareConsortium/ITK/archive/4d750726d06ba28c601b8a4bfac8780baa395ff1.zip
     directory: Documentation/docs
     description: "ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions"
     base_url: https://docs.itk.org
     format: markdown
   - name: ITK-Wasm
     id: itkwasm
-    source: https://github.com/InsightSoftwareConsortium/itk-wasm/archive/refs/heads/main.zip
+    source: https://github.com/InsightSoftwareConsortium/itk-wasm/archive/169a2e0eed6b30d91c59081643668ef13045bb93.zip
     directory: docs
     description: "High-performance spatial analysis in a web browser, Node.js, and across programming languages and hardware architectures"
     base_url: https://wasm.itk.org
     format: markdown
 
-
 additional_channels:
   - name: "biii.eu"
     id: biii.eu