Merge pull request #33 from the-virtual-brain/VT-35

VT-35: create user settings in jupyterlab

package.json

@@ -19,7 +19,8 @@
   "files": [
     "lib/**/*.{d.ts,eot,gif,html,jpg,js,js.map,json,png,svg,woff2,ttf}",
     "style/**/*.{css,js,eot,gif,html,jpg,json,png,svg,woff2,ttf}",
-    "style/index.js"
+    "style/index.js",
+    "schema/*.json"
   ],
   "main": "lib/index.js",
   "types": "lib/index.d.ts",
@@ -122,7 +123,8 @@
       }
     },
     "extension": true,
-    "outputDir": "tvb_ext_unicore/labextension"
+    "outputDir": "tvb_ext_unicore/labextension",
+    "schemaDir": "schema"
   },
   "jupyter-releaser": {
     "hooks": {

schema/settings.json

@@ -0,0 +1,15 @@
+{
+  "title": "Registry Setting",
+  "description": "Settings to define the registry you want to connect with the help of tvb-ext-unicore.",
+  "type": "object",
+  "properties": {
+    "registry": {
+      "type": "string",
+      "title": "Registry",
+      "description": "Provide a registry url.",
+      "default": "https://unicore.fz-juelich.de/HBP/rest/registries/default_registry"
+    }
+  },
+  "additionalProperties": false,
+  "type": "object"
+}

src/index.ts

@@ -28,6 +28,7 @@ import { NO_SITE, getJobCode } from './constants';
 import logoUnicore from '../style/icons/logo-unicore.svg';
 import { SideButton } from './components/SideButton';
 import { LabIcon } from '@jupyterlab/ui-components';
+import { ISettingRegistry } from '@jupyterlab/settingregistry';
 
 async function cancelJob(resource_url: string): Promise<any> {
   const dataToSend = { resource_url: resource_url };
@@ -59,7 +60,8 @@ const plugin: JupyterFrontEndPlugin<void> = {
     IConsoleTracker,
     ILabShell,
     INotebookTracker,
-    IFileBrowserFactory
+    IFileBrowserFactory,
+    ISettingRegistry
   ],
   activate: async (
     app: JupyterFrontEnd,
@@ -68,12 +70,28 @@ const plugin: JupyterFrontEndPlugin<void> = {
     consoleTracker: IConsoleTracker,
     labShell: ILabShell,
     notebookTracker: INotebookTracker,
-    factory: IFileBrowserFactory
+    factory: IFileBrowserFactory,
+    settingRegistry: ISettingRegistry
   ) => {
     console.log('JupyterLab extension tvb-ext-unicore is activated!');
     let widget: MainAreaWidget<PyunicoreWidget>;
     const columns = ['id', 'name', 'owner', 'site', 'status', 'start_time'];
     const command = 'tvb_ext_unicore:open';
+
+    // Load settings
+    console.log('SettingRegistry:', settingRegistry);
+    await settingRegistry
+      .load('tvb-ext-unicore:settings')
+      .then(settings => {
+        console.log('Settings loaded:', settings.composite);
+
+        const registry = settings.get('registry').composite as string;
+        console.log(`Registry: ${registry}`);
+      })
+      .catch(reason => {
+        console.error('Failed to load settings:', reason);
+      });
+
     app.commands.addCommand(command, {
       label: 'PyUnicore Task Stream',
       execute: async (args = { defaultSite: NO_SITE }): Promise<any> => {

tvb_ext_unicore/unicore_wrapper/unicore_wrapper.py

@@ -4,16 +4,17 @@
 #
 # (c) 2022-2024, TVB Widgets Team
 #
-
+import json
 import os
-from pyunicore.client import _HBP_REGISTRY_URL
+import requests
 import pyunicore.client as unicore_client
 from pyunicore.credentials import OIDCToken
 from requests.exceptions import ConnectionError
 from tvb_ext_unicore.exceptions import TVBExtUnicoreException, ClientAuthException, SitesDownException
 from tvb_ext_unicore.exceptions import FileNotExistsException, JobRunningException
 from tvb_ext_unicore.logger.builder import get_logger
 from tvb_ext_unicore.unicore_wrapper.job_dto import JobDTO
+from tvb_ext_unicore.utils import get_registry
 
 LOGGER = get_logger(__name__)
 DOWNLOAD_MESSAGE = 'Downloaded successfully!'
@@ -25,23 +26,33 @@ def __init__(self):
         token = self.__retrieve_token_str()
         token = OIDCToken(token)
         self.transport = self.__build_transport(token)
-        self.registry = unicore_client.Registry(self.transport, _HBP_REGISTRY_URL)
+        self.registry = unicore_client.Registry(self.transport, get_registry())
 
     def __retrieve_token_str(self):
         try:
+            # for ebrains lab
             from clb_nb_utils import oauth as clb_oauth
             token = clb_oauth.get_token()
         except (ModuleNotFoundError, ConnectionError) as e:
             LOGGER.warning(f"Could not connect to EBRAINS to retrieve an auth token: {e}")
-            LOGGER.info("Will try to use the auth token defined by environment variable CLB_AUTH...")
-
-            token = os.environ.get('CLB_AUTH')
-            if token is None:
-                LOGGER.error("No auth token defined as environment variable CLB_AUTH! Please define one!")
-                raise TVBExtUnicoreException("Cannot connect to EBRAINS HPC without an auth token! Either run this on "
-                                             "Collab, or define the CLB_AUTH environment variable!")
-
-            LOGGER.info("Successfully retrieved the auth token from environment variable CLB_AUTH!")
+            try:
+                # for juelich's lab
+                api_url = os.getenv("JUPYTERHUB_API_URL")
+                user_api_url = f"{api_url}/user_oauth"
+                headers = {"Authorization": "token {}".format(os.getenv("JUPYTERHUB_API_TOKEN"))}
+                r = requests.get(user_api_url, headers=headers)
+                response = json.loads(r.content.decode("utf-8"))
+                token = response["auth_state"]["access_token"]
+            except Exception as e:
+                LOGGER.warning(f"Could not connect to Juelich's JupyterLab to retrieve an auth token: {e}")
+                LOGGER.info("Will try to use the auth token defined by environment variable CLB_AUTH...")
+                token = os.environ.get('CLB_AUTH')
+                if token is None:
+                    LOGGER.error("No auth token defined as environment variable CLB_AUTH! Please define one!")
+                    raise TVBExtUnicoreException("Cannot connect to EBRAINS HPC without an auth token! Either run "
+                                                 "this on Collab, or define the CLB_AUTH environment variable!")
+
+                LOGGER.info("Successfully retrieved the auth token from environment variable CLB_AUTH!")
         return token
 
     def __build_transport(self, token):

tvb_ext_unicore/utils.py

@@ -7,7 +7,11 @@
 
 import json
 import enum
+import os
+
+from jupyter_core.paths import jupyter_config_dir
 from tvb_ext_unicore.logger.builder import get_logger
+from pyunicore.client import _HBP_REGISTRY_URL
 
 LOGGER = get_logger(__name__)
 
@@ -21,6 +25,25 @@ class DownloadStatus(str, enum.Enum):  # inherit str for json serialization
     SUCCESS = 'success'
 
 
+def get_user_settings():
+    data_dir = jupyter_config_dir()  # path to jupyter configs folder; usually it's $HOME/.jupyter
+    # path to user-settings for this extension
+    settings_path = os.path.join(data_dir, 'lab', 'user-settings', 'tvb-ext-unicore', 'settings.jupyterlab-settings')
+    if os.path.exists(settings_path):
+        with open(settings_path, 'r', encoding='utf-8') as f:
+            settings = json.load(f)
+    else:
+        settings = {}
+
+    return settings
+
+
+def get_registry():
+    user_settings = get_user_settings()
+    registry = user_settings.get('registry', _HBP_REGISTRY_URL)  # if registry is not set, use a default value
+    return registry
+
+
 def build_response(status, message):
     # type: (DownloadStatus, str) -> str
     """