Merge pull request #7 from kephale/main

Add support for dataset_ids CLI parameter and refactor serve functions

Author: kephale

README.md

@@ -1,27 +1,81 @@
-# Launch a server
+# Copick Server
 
+A server for [copick](https://github.com/kephale/copick) projects.
+
+## Installation
+
+```bash
+pip install .
 ```
-uv run copick_server/demo_server.py
+
+## Usage
+
+### Launch a server
+
+#### Using a config file
+
+```bash
+python -m copick_server.server serve --config path/to/copick_config.json --cors "*" --port 8000
 ```
 
-# Launch a client
+#### Using dataset IDs from CZ cryoET Data Portal
 
+```bash
+python -m copick_server.server serve --dataset-ids 10440 --cors "*" --port 8017
 ```
-uv run copick_server/client.py
+
+You can use multiple dataset IDs by repeating the option:
+
+```bash
+python -m copick_server.server serve --dataset-ids 10440 --dataset-ids 10441 --cors "*" --port 8017
 ```
 
-# Running Tests
+#### Using uv run
 
+With config file:
+```bash
+uv run copick_server/server.py serve --config ~/Data/copick/full_ml_challenge_czcdp.json --cors "*" --port 8017
 ```
+
+With dataset IDs:
+```bash
+uv run copick_server/server.py serve --dataset-ids 10440 --cors "*" --port 8017
+```
+
+### Launch a client
+
+```bash
+uv run copick_server/client.py
+```
+
+## Running Tests
+
+```bash
 pip install ".[test]"
 pytest
 ```
 
 For coverage report:
-```
+```bash
 pytest --cov=copick_server
 ```
 
-# References
+## CLI Options
+
+```
+python -m copick_server.server serve --help
+```
+
+| Option            | Description                                            | Default       |
+|-------------------|--------------------------------------------------------|---------------|
+| -c, --config      | Path to the configuration file                         | None          |
+| -ds, --dataset-ids| Dataset IDs to include in the project                  | None          |
+| --overlay-root    | Root URL for the overlay storage                       | /tmp/overlay_root |
+| --cors            | Origin to allow CORS. Use wildcard '*' to allow all    | None          |
+| --host            | Bind socket to this host                               | 127.0.0.1     |
+| --port            | Bind socket to this port                               | 8000          |
+| --reload          | Enable auto-reload                                     | False         |
+
+## References
 
-The idea is influenced by https://github.com/manzt/simple-zarr-server, but aimed at supporting https://github.com/copick/copick.
+The idea is influenced by https://github.com/manzt/simple-zarr-server, but aimed at supporting https://github.com/kephale/copick.

copick_server/client.py

@@ -4,13 +4,13 @@
 from fsspec import get_mapper
 
 # First read the tomogram to get the shape
-store = get_mapper("http://localhost:8000/14268/Tomograms/VoxelSpacing7.84/wbp.zarr")
+store = get_mapper("http://localhost:8017/16463/Tomograms/VoxelSpacing10.012/wbp.zarr")
 tomo = zarr.open(store, mode='r')
 full_shape = tomo["0"].shape
 print(f"Tomogram shape: {full_shape}")
 
 # Example parameters
-voxel_size = 7.84  # must match your tomogram's voxel spacing
+voxel_size = 10.012
 user_id = "kisharrington"
 session_id = "copickServer"
 name = "membrane"  # This must match a pickable object in your config
@@ -33,7 +33,7 @@
 data_bytes = shape_header + data.tobytes()
 
 # Send to server as a single request
-url = f"http://localhost:8000/14268/Segmentations/{seg_filename}"
+url = f"http://localhost:8017/16463/Segmentations/{seg_filename}"
 response = requests.put(url, data=data_bytes)
 
 if response.status_code == 200:

copick_server/demo_server.py

@@ -227,30 +227,54 @@ def create_copick_app(root: copick.models.CopickRoot, cors_origins: Optional[Lis
 
     return app
 
-def serve_copick(config_path: str, allowed_origins: Optional[List[str]] = None, **kwargs):
+def serve_copick(config_path: Optional[str] = None, dataset_ids: Optional[List[int]] = None, overlay_root: str = "/tmp/overlay_root", allowed_origins: Optional[List[str]] = None, **kwargs):
     """Start an HTTP server serving a Copick project.
     
     Parameters
     ----------
-    config_path : str
+    config_path : str, optional
         Path to Copick config file
+    dataset_ids : list of int, optional
+        Dataset IDs to include in the project
+    overlay_root : str, optional
+        Root URL for the overlay storage, default is "/tmp/overlay_root"
     allowed_origins : list of str, optional
         List of allowed CORS origins. Use ["*"] to allow all.
     **kwargs
         Additional arguments passed to uvicorn.run()
+        
+    Notes
+    -----
+    Either config_path or dataset_ids must be provided, but not both.
     """
-    root = copick.from_file(config_path)
+    if config_path and dataset_ids:
+        raise ValueError("Either config_path or dataset_ids must be provided, but not both.")
+    elif config_path:
+        root = copick.from_file(config_path)
+    elif dataset_ids:
+        root = copick.from_czcdp_datasets(
+            dataset_ids=dataset_ids,
+            overlay_root=overlay_root,
+            overlay_fs_args={"auto_mkdir": True},
+        )
+    else:
+        raise ValueError("Either config_path or dataset_ids must be provided.")
+        
     app = create_copick_app(root, allowed_origins)
     uvicorn.run(app, **kwargs)
     return app
 
-def serve_copick_threaded(config_path: str, allowed_origins: Optional[List[str]] = None, **kwargs):
+def serve_copick_threaded(config_path: Optional[str] = None, dataset_ids: Optional[List[int]] = None, overlay_root: str = "/tmp/overlay_root", allowed_origins: Optional[List[str]] = None, **kwargs):
     """Start an HTTP server in a background thread and return the app.
     
     Parameters
     ----------
-    config_path : str
+    config_path : str, optional
         Path to Copick config file
+    dataset_ids : list of int, optional
+        Dataset IDs to include in the project
+    overlay_root : str, optional
+        Root URL for the overlay storage, default is "/tmp/overlay_root"
     allowed_origins : list of str, optional
         List of allowed CORS origins. Use ["*"] to allow all.
     **kwargs
@@ -260,8 +284,24 @@ def serve_copick_threaded(config_path: str, allowed_origins: Optional[List[str]]
     -------
     app : FastAPI
         FastAPI application
+        
+    Notes
+    -----
+    Either config_path or dataset_ids must be provided, but not both.
     """
-    root = copick.from_file(config_path)
+    if config_path and dataset_ids:
+        raise ValueError("Either config_path or dataset_ids must be provided, but not both.")
+    elif config_path:
+        root = copick.from_file(config_path)
+    elif dataset_ids:
+        root = copick.from_czcdp_datasets(
+            dataset_ids=dataset_ids,
+            overlay_root=overlay_root,
+            overlay_fs_args={"auto_mkdir": True},
+        )
+    else:
+        raise ValueError("Either config_path or dataset_ids must be provided.")
+        
     app = create_copick_app(root, allowed_origins)
 
     # Start the server in a background thread
@@ -275,8 +315,36 @@ def serve_copick_threaded(config_path: str, allowed_origins: Optional[List[str]]
 
     return app
 
-@click.command()
-@click.argument("config", type=click.Path(exists=True))
+@click.group()
+@click.pass_context
+def cli(ctx):
+    pass
+
+
+@cli.command()
+@click.option(
+    "-c",
+    "--config",
+    type=click.Path(exists=True),
+    help="Path to the configuration file.",
+    required=False,
+    metavar="PATH",
+)
+@click.option(
+    "-ds",
+    "--dataset-ids",
+    type=int,
+    multiple=True,
+    help="Dataset IDs to include in the project (multiple inputs possible).",
+    metavar="ID",
+)
+@click.option(
+    "--overlay-root",
+    type=str,
+    default="/tmp/overlay_root",
+    help="Root URL for the overlay storage.",
+    show_default=True,
+)
 @click.option(
     "--cors",
     type=str,
@@ -298,15 +366,30 @@ def serve_copick_threaded(config_path: str, allowed_origins: Optional[List[str]]
     show_default=True,
 )
 @click.option("--reload", is_flag=True, default=False, help="Enable auto-reload.")
-def main(config: str, cors: Optional[str], host: str, port: int, reload: bool):
+@click.pass_context
+def serve(ctx, config: Optional[str] = None, dataset_ids: Optional[tuple] = None, overlay_root: str = "/tmp/overlay_root", cors: Optional[str] = None, host: str = "127.0.0.1", port: int = 8000, reload: bool = False):
     """Serve a Copick project over HTTP."""
-    serve_copick(
-        config,
-        allowed_origins=[cors] if cors else None,
-        host=host,
-        port=port,
-        reload=reload
-    )
+    if config and dataset_ids:
+        ctx.fail("Either --config or --dataset-ids must be provided, not both.")
+    elif not config and not dataset_ids:
+        ctx.fail("Either --config or --dataset-ids must be provided.")
+    
+    try:
+        serve_copick(
+            config_path=config,
+            dataset_ids=dataset_ids if dataset_ids else None,
+            overlay_root=overlay_root,
+            allowed_origins=[cors] if cors else None,
+            host=host,
+            port=port,
+            reload=reload
+        )
+    except Exception as e:
+        ctx.fail(f"Error serving Copick project: {str(e)}")
+
+
+def main():
+    cli()
 
 if __name__ == "__main__":
     main()

copick_server/server.py

@@ -6,7 +6,7 @@ readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
     "click",
-    "copick",
+    "copick>=1.0.1",
     "numpy",
     "uvicorn",
     "zarr",