Add server extension using h5grove to replace jupyterlab_hdf

.github/workflows/build.yml

@@ -39,7 +39,7 @@ jobs:
           pip install .
           jupyter lab build
           jupyter serverextension list 1>serverextensions 2>&1
-          cat serverextensions | grep "jupyterlab_hdf.*OK"
+          cat serverextensions | grep "jupyterlab_h5web.*OK"
           jupyter labextension list 1>labextensions 2>&1
           cat labextensions | grep "jupyterlab-h5web.*OK"
 

CONTRIBUTING.md

@@ -12,7 +12,7 @@ The `jlpm` command is JupyterLab's pinned version of
 
 # Install package in development mode
 pip install -e .
-# Ensure that `jupyterlab_hdf` server extension is present and enabled
+# Ensure that `jupyterlab_h5web` server extension is present and enabled
 jupyter serverextension list
 
 # Install dependencies
@@ -51,8 +51,7 @@ This extension uses `prettier` to format `*.ts` files and `black` to format
 
 ### Why a Python package for a front-end extension ?
 
-1. To ease up installation (e.g. automatic resolution of the `jupyter_hdf` PyPI
-   package)
+1. To ease up installation
 2. To get ready to release a pre-built extension (_JupyterLab 3_)
 
 The pre-built extension will indeed remove the need for `node`. For _JupyterLab

README.md

@@ -116,29 +116,23 @@ See https://github.com/silx-kit/jupyterlab-h5web/releases.
 ### Check the server extension
 
 If you are seeing the frontend extension but it is not working, check that
-`jupyterlab_hdf` is installed and enabled.
+`jupyterlab_h5web` is installed and enabled.
 
 It should be listed when running:
 
 ```bash
 jupyter serverextension list
 ```
 
-If `jupyterlab_hdf` does not appear, try to install it manually:
+If `jupyterlab_h5web` does not appear or is disabled, try to enable it:
 
 ```
-pip install jupyterlab_hdf
-```
-
-and to enable it:
-
-```
-jupyter serverextension enable jupyterlab_hdf
+jupyter serverextension enable jupyterlab_h5web
 ```
 
 ### Check the frontend extension
 
-If `jupyterlab_hdf` is installed and enabled but you are not seeing the
+If `jupyterlab_h5web` is installed and enabled but you are not seeing the
 frontend, check the frontend is installed:
 
 ```bash

jupyter-config/jupyterlab-h5web.json

@@ -1,7 +1,7 @@
 {
   "NotebookApp": {
     "nbserver_extensions": {
-      "jupyterlab_hdf": true
+      "jupyterlab_h5web": true
     }
   }
 }

jupyterlab_h5web/__init__.py

@@ -1 +1,24 @@
 from .widget import H5Web
+
+
+def _jupyter_server_extension_points():
+    return [{"module": "jupyterlab_h5web"}]
+
+
+def _load_jupyter_server_extension(server_app):
+    """Registers the API handler to receive HTTP requests from the frontend extension.
+    Parameters
+    ----------
+    server_app: jupyterlab.labapp.LabApp
+        JupyterLab application instance
+    """
+    from .handlers import setup_handlers
+
+    setup_handlers(server_app.web_app, server_app.notebook_dir)
+    server_app.log.info(
+        f"Jupyterlab-h5web extension will serve HDF5 files from {server_app.notebook_dir}"
+    )
+
+
+# For backward compatibility with notebook server - useful for Binder/JupyterHub
+load_jupyter_server_extension = _load_jupyter_server_extension

jupyterlab_h5web/handlers.py

@@ -0,0 +1,71 @@
+import h5py
+import tornado.web
+from jupyter_server.base.handlers import APIHandler
+from jupyter_server.utils import url_path_join
+
+from h5grove.encoders import encode
+from h5grove.content import create_content, ResolvedEntityContent, DatasetContent
+
+from .utils import resolve_file_path
+
+
+class BaseHandler(APIHandler):
+    def initialize(self, base_dir) -> None:
+        self.base_dir = base_dir
+
+    @tornado.web.authenticated
+    def get(self, file_path):
+        path = self.get_query_argument("path", None)
+        format = self.get_query_argument("format", None)
+
+        with h5py.File(resolve_file_path(file_path, self.base_dir), "r") as h5file:
+            content = self.get_content(h5file, path)
+
+        encoded_content_chunks, headers = encode(content, format)
+
+        for key, value in headers.items():
+            self.set_header(key, value)
+        for chunk in encoded_content_chunks:
+            self.write(chunk)
+        self.finish()
+
+    def get_content(self, h5file, path):
+        raise NotImplementedError
+
+
+class AttributeHandler(BaseHandler):
+    def get_content(self, h5file, path):
+        content = create_content(h5file, path)
+        assert isinstance(content, ResolvedEntityContent)
+        return content.attributes()
+
+
+class DataHandler(BaseHandler):
+    def get_content(self, h5file, path):
+        selection = self.get_query_argument("selection", None)
+
+        content = create_content(h5file, path)
+        assert isinstance(content, DatasetContent)
+        return content.data(selection)
+
+
+class MetadataHandler(BaseHandler):
+    def get_content(self, h5file, path):
+        content = create_content(h5file, path)
+        return content.metadata()
+
+
+def setup_handlers(web_app, base_dir):
+    pattern = "(.*)"
+    endpoints = {"attr": AttributeHandler, "data": DataHandler, "meta": MetadataHandler}
+
+    handlers = [
+        (
+            url_path_join(web_app.settings["base_url"], "h5web", endpoint, pattern),
+            handler,
+            {"base_dir": base_dir},
+        )
+        for endpoint, handler in endpoints
+    ]
+
+    web_app.add_handlers(pattern, handlers)

jupyterlab_h5web/utils.py

@@ -0,0 +1,21 @@
+from pathlib import Path
+from typing import Union
+
+
+def _resolve_path(file_path: Path, base_dir: Path) -> Path:
+    if file_path.is_absolute():
+        return file_path
+
+    return base_dir / file_path
+
+
+def resolve_file_path(
+    file_path: Union[str, Path], base_dir: Union[str, Path]
+) -> Union[str, Path]:
+    path = file_path if isinstance(file_path, Path) else Path(file_path)
+    base = base_dir if isinstance(base_dir, Path) else Path(base_dir)
+
+    if isinstance(file_path, Path):
+        return str(_resolve_path(path, base))
+
+    return _resolve_path(path, base)

jupyterlab_h5web/widget.py

@@ -1,3 +1,5 @@
+from jupyterlab_h5web.utils import resolve_file_path
+import os
 import os.path
 from pathlib import Path
 from typing import Dict, Tuple, Union
@@ -9,10 +11,11 @@ class H5Web(DisplayObject):
 
     def __init__(self, data: Union[str, Path], **kwargs) -> None:
         # "Data" here is the path to the HDF5 file.
-        self.data = data
+        self.data = resolve_file_path(data, os.getcwd())
         self.metadata = {}
         if kwargs:
             self.metadata.update(kwargs)
+        self._check_data()
 
     def _check_data(self) -> None:
         if not os.path.isfile(self.data):

package.json

@@ -45,7 +45,7 @@
     "postversion": "git push && git push --tags"
   },
   "dependencies": {
-    "@h5web/app": "0.0.18",
+    "@h5web/app": "0.0.23",
     "@jupyterlab/application": "^2.0.0 || ^3.0.0",
     "@jupyterlab/apputils": "~2.3.0 || ^3.0.5",
     "@jupyterlab/coreutils": "^4.0.0 || ^5.0.0",
@@ -76,16 +76,6 @@
     "style/*.css"
   ],
   "jupyterlab": {
-    "discovery": {
-      "server": {
-        "managers": [
-          "pip"
-        ],
-        "base": {
-          "name": "jupyterlab_hdf"
-        }
-      }
-    },
     "extension": true
   }
 }

setup.py

@@ -58,7 +58,7 @@
     long_description_content_type="text/markdown",
     cmdclass=cmdclass,
     packages=setuptools.find_packages(),
-    install_requires=["jupyterlab_hdf"],
+    install_requires=["jupyter_server>=1.6,<2", "h5grove"],
     extras_require={"full": ["hdf5plugin"]},
     python_requires=">=3.6",
     zip_safe=False,

src/H5webApp.tsx

@@ -1,5 +1,5 @@
 import React, { useEffect, useState } from 'react';
-import { App, JupyterProvider } from '@h5web/app';
+import { App, H5CoreProvider as H5GroveProvider } from '@h5web/app';
 import { ServerConnection } from '@jupyterlab/services';
 
 // Render the App twice on mount as the CSS is not loaded at first render.
@@ -23,12 +23,12 @@ function H5webApp(props: { filePath: string }) {
 
   return (
     <div className="h5web-root">
-      <JupyterProvider
-        url={baseUrl.endsWith('/') ? baseUrl.slice(0, -1) : baseUrl}
+      <H5GroveProvider
+        url={`${baseUrl.endsWith('/') ? baseUrl.slice(0, -1) : baseUrl}/h5web`}
         filepath={filePath}
       >
         <TwoRenderApp />
-      </JupyterProvider>
+      </H5GroveProvider>
     </div>
   );
 }