@galaxyproject/jupyterlite 0.0.3 → 0.0.5

package/README.md

@@ -1,39 +1,47 @@
-# JupyterLite + Pyodide Setup
+# JupyterLite + Galaxy Integration
 
 This project integrates JupyterLite with the Pyodide kernel and custom extensions such as `jl-galaxy`.
 
+The `jl-galaxy` extension enables Jupyter users to interact seamlessly with their Galaxy history — including loading and saving notebooks — through a fully integrated browser-based interface.
+
 ## ⚙️ Requirements
 
-- Python 3.7+
-- Node.js 16+
-- npm 7+
+- Python **3.10.17+**
+- Node.js **20.19.1+**
+- npm **10.8.2+**
 
-## 📦 Installation
+---
 
-### 1. Set up Python dependencies
+## 📦 Setup Instructions
 
-Install JupyterLite and the Pyodide kernel plugin:
+### 1. Create and activate a virtual environment
 
 ```bash
-pip install jupyterlite
-pip install jupyterlite-pyodide-kernel
+python -m venv .venv
+source .venv/bin/activate
 ```
 
-> These packages provide the CLI and register the Pyodide kernel for bundling.
+### 2. Install Python dependencies
+
+```bash
+pip install -r requirements.txt
+```
 
-### 2. Set up Node dependencies
+This installs `jupyterlite`, `jupyterlite-pyodide-kernel`, and the `gxy` utility module for Galaxy integration.
 
-Install JavaScript dependencies (for building extensions):
+### 3. Install Node.js dependencies
 
 ```bash
 npm install
 ```
 
-This installs dependencies listed in `package.json`, such as custom JupyterLite extensions.
+This installs JavaScript dependencies listed in `package.json`, including custom JupyterLite extensions.
+
+---
 
 ## 🔨 Build
 
-Run the build to generate a standalone JupyterLite distribution:
+Run the full build to generate a standalone JupyterLite distribution:
 
 ```bash
 npm run build
@@ -42,29 +50,92 @@ npm run build
 This will:
 - Run `jupyter lite build`
 - Include the Pyodide kernel
-- Bundle your extensions (e.g., `jl-galaxy`)
-- Generate the final site in `./static/dist/_output`
+- Bundle federated extensions like `jl-galaxy`
+- Output the final static site to: `./static/dist/_output`
+
+---
 
-## 🚀 Launch
+## 🚀 Serve
 
-You can serve the output using any static file server. For quick testing:
+To serve the JupyterLite site locally:
 
 ```bash
-npx serve static/dist/_output
+npm run serve
 ```
 
-Or use Python:
+Then open [http://localhost:3000](http://localhost:3000) in your browser.
 
-```bash
-cd static/dist/_output
-python -m http.server
+---
+
+## 🧰 Galaxy Integration Utilities (`gxy`)
+
+The `gxy` module provides Python functions to interact with the Galaxy API directly from JupyterLite.
+
+### ✅ `api(endpoint, method="GET", data=None)`
+Makes an HTTP request to a Galaxy API endpoint and returns the parsed JSON response.
+
+```python
+await api("/api/histories")
+await api("/api/histories", method="POST", data={"name": "New History"})
 ```
 
-Then open [http://localhost:8000](http://localhost:8000) in your browser.
+---
+
+### ✅ `get(datasets_identifiers, identifier_type="hid", retrieve_datatype=False)`
+Downloads dataset(s) by HID, ID, or regex pattern. Saves them to Pyodide's virtual filesystem.
+
+```python
+await get(3)                          # by HID
+await get("some_id", identifier_type="id")
+await get("myfile.*", identifier_type="regex")
+```
 
 ---
 
-## 💡 Notes
+### ✅ `put(name, output=None, ext="auto", dbkey="?", history_id=None)`
+Uploads a file from the virtual filesystem to the current Galaxy history.
+
+```python
+await put("mydata.txt", "newname.txt", ext="txt")
+```
+
+---
+
+### ✅ `get_history(history_id=None)`
+Returns metadata for all visible datasets in the current history.
+
+```python
+await get_history()
+```
+
+---
+
+### ✅ `get_history_id()`
+Returns the current history ID based on the dataset context.
+
+```python
+await get_history_id()
+```
+
+---
+
+### ✅ `get_environment()`
+Returns the Galaxy environment injected into the session via `__gxy__`.
+
+```python
+get_environment()
+```
+
+---
+
+### ✅ `_find_matching_ids(history_datasets, list_of_regex_patterns, identifier_type='hid')`
+Used internally to resolve regex patterns to dataset identifiers.
+
+---
+
+## 📎 Notes
+
+- The `jl-galaxy` extension allows users to browse and manage Galaxy histories directly from the Jupyter UI.
+- All files must be placed within `static/dist/_output`; writing outside this directory breaks the build.
+- The upload helper uses `XMLHttpRequest` to work around Pyodide's limitations with `fetch`.
 
-- The build process automatically configures the Pyodide kernel and registers it as a federated extension.
-- If you're developing additional extensions, make sure to register them in `jupyter-lite.json` under `federated_extensions`.

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@galaxyproject/jupyterlite",
-    "version": "0.0.3",
+    "version": "0.0.5",
     "type": "module",
     "files": [
         "static/dist"

package/static/dist/_output/jupyter-lite.json

@@ -5,6 +5,21 @@
     "appVersion": "0.5.1",
     "baseUrl": "./",
     "defaultKernelName": "python",
+    "disabledExtensions": [
+      "@jupyterlab/filebrowser-extension",
+      "@jupyterlab/launcher-extension",
+      "@jupyterlab/running-extension",
+      "@jupyterlab/toc-extension",
+      "@jupyterlab/fileeditor-extension:plugin",
+      "@jupyterlab/fileeditor-extension:cursor-position",
+      "@jupyterlab/fileeditor-extension:completer",
+      "@jupyterlab/fileeditor-extension:language-server",
+      "@jupyterlab/fileeditor-extension:editor-syntax-status",
+      "@jupyterlab/fileeditor-extension:tab-space-status",
+      "@jupyterlab/notebook-extension:toc",
+      "@jupyterlite/application-extension:share-file",
+      "@jupyterlab/tooltip-extension:files"
+    ],
     "faviconUrl": "./lab/favicon.ico",
     "federated_extensions": [
       {
@@ -13,17 +28,17 @@
         "load": "static/remoteEntry.3ac7f76fb22d01270496.js",
         "name": "@jupyterlite/pyodide-kernel-extension"
       },
+      {
+        "extension": "./extension",
+        "load": "entry.js",
+        "name": "jl-galaxy"
+      },
       {
         "extension": "./extension",
         "liteExtension": false,
         "load": "static/remoteEntry.5cbb9d2323598fbda535.js",
         "name": "jupyterlab_pygments",
         "style": "./style"
-      },
-      {
-        "name": "jl-galaxy",
-        "load": "entry.js",
-        "extension": "./extension"
       }
     ],
     "fileTypes": {
@@ -310,22 +325,7 @@
           ]
         }
       }
-    },
-    "disabledExtensions": [
-      "@jupyterlab/filebrowser-extension",
-      "@jupyterlab/launcher-extension",
-      "@jupyterlab/running-extension",
-      "@jupyterlab/toc-extension",
-      "@jupyterlab/fileeditor-extension:plugin",
-      "@jupyterlab/fileeditor-extension:cursor-position",
-      "@jupyterlab/fileeditor-extension:completer",
-      "@jupyterlab/fileeditor-extension:language-server",
-      "@jupyterlab/fileeditor-extension:editor-syntax-status",
-      "@jupyterlab/fileeditor-extension:tab-space-status",
-      "@jupyterlab/notebook-extension:toc",
-      "@jupyterlite/application-extension:share-file",
-      "@jupyterlab/tooltip-extension:files"
-    ]
+    }
   },
   "jupyter-lite-schema-version": 0
 }

package/static/dist/_output/pypi/all.json

@@ -0,0 +1,28 @@
+{
+  "gxy": {
+    "releases": {
+      "0.0.0": [
+        {
+          "comment_text": "",
+          "digests": {
+            "md5": "aaaf4a39a1b09914421e1217fdd80ad9",
+            "sha256": "6a71c41fcd17283c8259d1011e8c5f8e297850357594c7c20407720d4985d05f"
+          },
+          "downloads": -1,
+          "filename": "gxy-0.0.0-py3-none-any.whl",
+          "has_sig": false,
+          "md5_digest": "aaaf4a39a1b09914421e1217fdd80ad9",
+          "packagetype": "bdist_wheel",
+          "python_version": "py3",
+          "requires_python": ">=3.7",
+          "size": 3919,
+          "upload_time": "2025-05-09T17:32:52.344251Z",
+          "upload_time_iso_8601": "2025-05-09T17:32:52.344251Z",
+          "url": "./gxy-0.0.0-py3-none-any.whl",
+          "yanked": false,
+          "yanked_reason": null
+        }
+      ]
+    }
+  }
+}