Merge branch 'chatbot_extension' into main

.github/workflows/docker-publish.yml

@@ -0,0 +1,35 @@
+name: Build and Publish Docker Image
+
+on:
+  push:
+    branches:
+      - main  # Trigger the workflow on pushes to the main branch
+  pull_request:
+    branches:
+      - main  # Trigger the workflow on pull requests to the main branch
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/[email protected]
+        with:
+          fetch-depth: 2
+
+      - name: Log in to the Container registry
+        uses: docker/[email protected]
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push Docker image (latest tag)
+        uses: docker/[email protected]
+        with:
+          context: .
+          file: Dockerfile
+          push: true
+          tags: ghcr.io/${{ github.repository }}:latest
+          labels: |
+            org.opencontainers.image.source=${{ github.server_url }}/${{ github.repository }}

.gitignore

@@ -4,7 +4,6 @@ __pycache__/
 *.egg-info/
 build/
 dist/
-docs/
 user_docs/
 tests/cache
 tests/generated_json_schemas

Dockerfile

@@ -0,0 +1,40 @@
+# Use an image with Python 3.11
+FROM python:3.11-slim
+
+# Set the working directory
+WORKDIR /app/
+
+# Create a non-root user
+RUN groupadd -r bioimageio_colab && useradd -r -g bioimageio_colab bioimageio_colab
+
+# Install necessary system packages
+RUN apt-get update && apt-get install -y \
+    curl \
+    jq \
+    && rm -rf /var/lib/apt/lists/*
+
+# Upgrade pip
+RUN pip install --upgrade pip
+
+# Copy the requirements file for SAM to the docker environment
+COPY ./requirements.txt /app/requirements.txt
+COPY ./requirements-sam.txt /app/requirements-sam.txt
+
+# Install the required packages for SAM
+RUN pip install -r /app/requirements-sam.txt
+
+# Copy the python script to the docker environment
+COPY ./bioimageio_colab/register_sam_service.py /app/register_sam_service.py
+
+# Change ownership of the application directory to the non-root user
+RUN chown -R bioimageio_colab:bioimageio_colab /app/
+
+# Fetch the Hypha server version and reinstall or upgrade hypha-rpc to the matching version
+RUN HYPHA_VERSION=$(curl -s https://hypha.aicell.io/config.json | jq -r '.hypha_version') && \
+    pip install --upgrade "hypha-rpc<=$HYPHA_VERSION"
+
+# Switch to the non-root user
+USER bioimageio_colab
+
+# Register the segmentation model as a hypha service
+ENTRYPOINT ["python", "register_sam_service.py"]

bioimageio_colab/create_workspace.py

@@ -0,0 +1,118 @@
+import argparse
+from hypha_rpc import connect_to_server, login
+import asyncio
+
+
+async def create_workspace_token(args):
+    # Get a user login token
+    token = await login({"server_url": args.server_url})
+
+    # Connect to the Hypha server
+    server = await connect_to_server(
+        {
+            "server_url": args.server_url,
+            "token": token,
+        }
+    )
+
+    # Check if the workspace already exists
+    user_workspaces = await server.list_workspaces()
+    exists = any(
+        [args.workspace_name == workspace["name"] for workspace in user_workspaces]
+    )
+
+    # Create a workspace
+    if not exists or args.overwrite:
+        workspace = await server.create_workspace(
+            {
+                "name": args.workspace_name,
+                "description": args.description,
+                "owners": args.owners,
+                "allow_list": args.allow_list,
+                "deny_list": args.deny_list,
+                "visibility": "public",  # public/protected
+                "persistent": True,  # keeps the workspace alive even after a server restart
+            },
+            overwrite=args.overwrite,
+        )
+        # Check if the workspace was created
+        assert any(
+            [
+                args.workspace_name == workspace["name"]
+                for workspace in await server.list_workspaces()
+            ]
+        )
+        print(f"Workspace created: {workspace['name']}")
+    else:
+        print(f"Workspace already exists: {args.workspace_name}")
+
+    # Connect to the workspace
+    server = await connect_to_server(
+        {
+            "server_url": args.server_url,
+            "token": token,
+            "workspace": args.workspace_name,
+        }
+    )
+
+    # List workspace services
+    services = await server.list_services()
+    if len(services) == 0:
+        print("No services in workspace")
+    else:
+        print("Services in workspace:")
+        for service in services:
+            print(f"- {service['name']}")
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Create the BioImageIO Colab workspace."
+    )
+    parser.add_argument(
+        "--server_url",
+        default="https://hypha.aicell.io",
+        type=str,
+        help="URL of the Hypha server",
+    )
+    parser.add_argument(
+        "--workspace_name",
+        default="bioimageio-colab",
+        type=str,
+        help="Name of the workspace",
+    )
+    parser.add_argument(
+        "--description",
+        default="The BioImageIO Colab workspace for serving interactive segmentation models.",
+        type=str,
+        help="Description of the workspace",
+    )
+    parser.add_argument(
+        "--owners",
+        nargs="+",
+        default=[],
+        type=str,
+        help="User emails that own the workspace",  # user email of workspace creator is added automatically
+    )
+    parser.add_argument(
+        "--allow_list",
+        nargs="+",
+        default=[],
+        type=str,
+        help="User emails allowed access to the workspace",
+    )
+    parser.add_argument(
+        "--deny_list",
+        nargs="+",
+        default=[],
+        type=str,
+        help="User emails denied access to the workspace",
+    )
+    parser.add_argument(
+        "--overwrite",
+        action="store_true",
+        default=False,
+        help="Overwrite the workspace if it already exists",
+    )
+
+    args = parser.parse_args()
+    asyncio.run(create_workspace_token(args))

bioimageio_colab_server/annotation_server.py → bioimageio_colab/data_provider.py

@@ -7,11 +7,11 @@
 import numpy as np
 import requests
 import shutil
-from imjoy_rpc.hypha import connect_to_server
+from hypha_rpc import connect_to_server
 from kaibu_utils import features_to_mask
 from tifffile import imread, imwrite
 
-from bioimageio_colab_server.hypha_data_store import HyphaDataStore
+from bioimageio_colab.hypha_data_store import HyphaDataStore
 
 logger = getLogger(__name__)
 logger.setLevel("INFO")
@@ -84,26 +84,31 @@ def download_labels(ds, data_folder):
 
 
 async def start_server(
-    data_url: str, path2data: str = "./data", outpath: str = "./kaibu_annotations"
+    path2data: str = "./data",
+    outpath: str = "./kaibu_annotations",
+    data_url: str = None,
 ):
     """
     Start the SAM annotation server.
 
-    When multiple people open the link, they can join a common workspace as an ImJoy client
+    When multiple people open the link, they can join a common workspace as an hypha client
     """
-    # Check if the data is available
     path2data = os.path.abspath(path2data)
-    if not os.path.exists(path2data):
-        # Create the path
-        os.makedirs(path2data)
-        # Download the data
-        save_path = os.path.join(path2data, data_url.split("/")[-1])
-        download_zip(data_url, save_path)
-        # Unzip the data
-        unzip_file(save_path, path2data)
-        # Remove the zip file
-        os.remove(save_path)
-        logger.info(f"Removed {save_path}")
+    if data_url is not None:
+        # Check if the data is available
+        if not os.path.exists(path2data):
+            # Create the path
+            os.makedirs(path2data)
+            # Download the data
+            save_path = os.path.join(path2data, data_url.split("/")[-1])
+            download_zip(data_url, save_path)
+            # Unzip the data
+            unzip_file(save_path, path2data)
+            # Remove the zip file
+            os.remove(save_path)
+            logger.info(f"Removed {save_path}")
+        else:
+            logger.info(f"Data already exists at {path2data}")
 
     # Create the output paths
     path2source = os.path.abspath(os.path.join(outpath, "source"))
@@ -112,7 +117,7 @@ async def start_server(
     os.makedirs(path2label, exist_ok=True)
 
     # Connect to the server link
-    server_url = "https://ai.imjoy.io"
+    server_url = "https://hypha.aicell.io"
     server = await connect_to_server({"server_url": server_url})
 
     # Upload to hypha.
@@ -127,7 +132,10 @@ async def start_server(
         {
             "name": "Collaborative Annotation",
             "id": "bioimageio-colab-annotation",
-            "config": {"visibility": "public", "run_in_executor": True},  # make protected
+            "config": {
+                "visibility": "public",  # TODO: make protected
+                "run_in_executor": True,
+            },
             # Exposed functions:
             # get a random image from the dataset
             # returns the image as a numpy image
@@ -142,13 +150,12 @@ async def start_server(
         }
     )
     annotation_sid = svc["id"]
-    model_sid = "oNwLbCSSNbiWrpr7h85F9f/ardFE2rx8wFB69JbbUGFfp:bioimageio-colab-model"
-    config_str = f'{{"server_url": "{server_url}", "annotation_service_id": "{annotation_sid}", "model_service_id": "{model_sid}", "token": "{token}"}}'
+    config_str = f'{{"server_url": "{server_url}", "annotation_service_id": "{annotation_sid}", "token": "{token}"}}'
     encoded_config = urllib.parse.quote(
         config_str, safe="/", encoding=None, errors=None
     )
     annotator_url = (
-        "https://imjoy.io/lite?plugin=https://raw.githubusercontent.com/bioimage-io/bioimageio-colab/kubernetes/plugins/bioimageio-colab-annotator.imjoy.html&config="
+        "https://imjoy.io/lite?plugin=https://raw.githubusercontent.com/bioimage-io/bioimageio-colab/chatbot_extension/plugins/bioimageio-colab-annotator.imjoy.html&config="
         + encoded_config
     )
     print("-" * 80)
@@ -161,6 +168,8 @@ async def start_server(
     )
     print("-" * 80)
 
+    return annotator_url
+
 
 if __name__ == "__main__":
     import asyncio

bioimageio_colab_server/hypha_data_store.py → bioimageio_colab/hypha_data_store.py

@@ -112,8 +112,8 @@ def remove(self, obj_id: str):
             return True
         raise IndexError("Not found: " + obj_id)
 
-async def test_data_store(server_url="https://ai.imjoy.io"):
-    from imjoy_rpc.hypha import connect_to_server, login
+async def test_data_store(server_url="https://hypha.aicell.io"):
+    from hypha_rpc import connect_to_server, login
     token = await login({"server_url": server_url})
     server = await connect_to_server({"server_url": server_url, "token": token})