Merge pull request #61 from the-virtual-brain/VT-40

VT-40. Create user settings file to set base folders for open viewer&script functionalities

package.json

@@ -19,7 +19,8 @@
   "files": [
     "lib/**/*.{d.ts,eot,gif,html,jpg,js,js.map,json,png,svg,woff2,ttf}",
     "style/**/*.{css,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",

schema/settings.json

@@ -0,0 +1,21 @@
+{
+  "title": "Base Directory Setting",
+  "description": "Setting to define the base directory.",
+  "type": "object",
+  "properties": {
+    "baseDirectoryWeb": {
+      "type": "string",
+      "title": "Base Directory Web",
+      "description": "for web",
+      "default": "."
+    },
+    "baseDirectoryKernel": {
+      "type": "string",
+      "title": "Base Directory Kernel",
+      "description": "for kernel",
+      "default": "."
+    }
+  },
+  "additionalProperties": false,
+  "type": "object"
+}

src/index.tsx

@@ -33,6 +33,7 @@ import type { Signal } from "@lumino/signaling";
 import { commandIDs } from "./commands/CommandIDs";
 import { IEditorTracker } from '@jupyterlab/fileeditor';
 import { IMainMenu } from '@jupyterlab/mainmenu';
+import { ISettingRegistry } from '@jupyterlab/settingregistry';
 
 const FACTORY = 'Xircuits editor';
 
@@ -59,6 +60,7 @@ const xircuits: JupyterFrontEndPlugin<void> = {
     ILayoutRestorer,
     IRenderMimeRegistry,
     IDocumentManager,
+    ISettingRegistry,
     IMainMenu,
     ITranslator,
     IEditorTracker,
@@ -71,6 +73,7 @@ const xircuits: JupyterFrontEndPlugin<void> = {
     restorer: ILayoutRestorer,
     rendermime: IRenderMimeRegistry,
     docmanager: IDocumentManager,
+    settingRegistry: ISettingRegistry,
     mainMenu?: IMainMenu,
     translator?: ITranslator,
     editorTracker?: IEditorTracker,
@@ -125,6 +128,21 @@ const xircuits: JupyterFrontEndPlugin<void> = {
       icon: xircuitsIcon
     });
 
+    // Load settings
+    console.log('SettingRegistry:', settingRegistry);
+    await settingRegistry
+      .load('tvb-ext-xircuits:settings')
+      .then(settings => {
+        console.log('Settings loaded:', settings.composite);
+
+        const baseDirWeb = settings.get('baseDirectoryWeb').composite as string;
+        const baseDirKernel = settings.get('baseDirectoryKernel').composite as string;
+        console.log(`Base Directory Web: ${baseDirWeb} & Base Directory Kernel: ${baseDirKernel}`);
+      })
+      .catch(reason => {
+        console.error('Failed to load settings:', reason);
+      });
+
     // Registering the widget factory
     app.docRegistry.addWidgetFactory(widgetFactory);
 

tvbextxircuits/handlers/user_config.py

@@ -1,8 +1,14 @@
 import json
+from pathlib import Path
 import tornado
 from jupyter_server.base.handlers import APIHandler
 import os
+
+from tvbextxircuits.logger.builder import get_logger
 from tvbextxircuits.nb_generator import IS_WINDOWS
+from tvbextxircuits.utils import get_base_dir_web, get_base_dir_kernel
+
+LOGGER = get_logger(__name__)
 
 
 class HomeDirectoryHandler(APIHandler):
@@ -17,14 +23,18 @@ def post(self):
         input_data = self.get_json_body()
 
         try:
-            # TODO: temporary hack for debug purposes on juwels, also handle the other operating systems(not just
-            #  windows)
             path = input_data["node_path"]
+            LOGGER.info(f'Component script path is: {path}')
+
             if IS_WINDOWS:
                 self.finish(json.dumps({"homeDirectory": path}))
             else:
-                home_directory = os.path.expanduser(os.path.join('~', path))
-                self.finish(json.dumps({"homeDirectory": home_directory}))
+                base_dir_web = get_base_dir_web()
+                home_directory = os.path.join(base_dir_web, path)
+                base_dir_kernel = get_base_dir_kernel()
+                return_path = str(Path(home_directory).relative_to(Path(base_dir_kernel)))
+                LOGGER.info(f'Opening component script from path: {return_path}')
+                self.finish(json.dumps({"homeDirectory": return_path}))
         except KeyError:
             data = {"error_msg": "Could not determine path from POST params!"}
             self.finish(json.dumps(data))

tvbextxircuits/nb_generator.py

@@ -12,9 +12,12 @@
 import importlib
 from tvb.simulator.integrators import HeunDeterministic
 from tvb.simulator.models.oscillator import Generic2dOscillator
+
+from tvbextxircuits.utils import get_base_dir_web, get_base_dir_kernel
 from xai_components.base_tvb import ComponentWithWidget
 
 from xai_components.logger.builder import get_logger
+from pathlib import Path
 
 LOGGER = get_logger(__name__)
 IS_WINDOWS = sys.platform.startswith('win')
@@ -101,25 +104,29 @@ def get_notebook_for_component(component_name, component_id, component_path, com
     def store(notebook, component_name, xircuits_id):
         file_name = f'{component_name}_widget.ipynb'
 
-        notebook_dir = os.path.join(NOTEBOOKS_DIR, xircuits_id)
+        base_dir_web = get_base_dir_web()
+
+        notebook_dir = os.path.join(base_dir_web, NOTEBOOKS_DIR, xircuits_id)
         if not os.path.exists(notebook_dir):
-            os.mkdir(notebook_dir)
+            os.makedirs(notebook_dir, exist_ok=True)
 
         path = os.path.join(notebook_dir, file_name)
 
         with open(path, 'w') as f:
             nbformat.write(notebook, f)
+
+        LOGGER.info(f'Writing notebook complete at path: {path}')
+
+        base_dir_kernel = get_base_dir_kernel()
+
+        return_path = str(Path(path).relative_to(Path(base_dir_kernel)))
 
         if IS_WINDOWS:
-            return NOTEBOOKS_DIR + '/' + xircuits_id + '/' + file_name
-
-        x = os.path.join(notebook_dir, file_name)
-        # TODO: temporary hack for debug purposes on juwels
-        # if juwels:
-        #     return os.relativeto(os.abspath(x), 'juwels')
-        return os.path.expanduser(os.path.join('~',  x))
-        # else:
-        #     return x
+            windows_expanded_path = return_path.replace("\\", "/")
+            LOGGER.info(f'Storing notebook on Windows at path: {windows_expanded_path}')
+            return windows_expanded_path
+
+        return return_path
 
 
 class NotebookGenerator(object):

tvbextxircuits/utils.py

@@ -1,12 +1,19 @@
+import json
 from pathlib import Path
 
+from jupyter_core.paths import jupyter_config_dir
+
+from tvbextxircuits.logger.builder import get_logger
+
 STORAGE_CONFIG_FILE = 'storage_config.json'  # To be used only for HPC runs
 COLLAB_NAME_KEY = 'collab_name'  # Used only for HPC runs
 BUCKET_NAME_KEY = 'bucket_name'  # Used only for HPC runs
 FOLDER_PATH_KEY = 'folder_path'  # Used only for HPC runs
 STORE_RESULTS_DIR = 'results'  # Used by component that takes care of storing data and stage-out from HPC
 DIR_TIME_STAMP_FRMT = '%Y.%m.%d_%H_%M_%S'
 
+LOGGER = get_logger(__name__)
+
 import os
 import urllib.parse
 import shutil
@@ -39,3 +46,32 @@ def copy_from_installed_wheel(package_name, resource="", dest_path=None, version
                 if config_path.exists():
                     shutil.rmtree(config_path)
                 shutil.copytree(resource_path, dest_path)
+
+
+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-xircuits', '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_base_dir_web():
+    user_settings = get_user_settings()
+    base_dir = user_settings.get('baseDirectoryWeb', '.')  # if baseDirectory is not set, use a default value
+    LOGGER.info(f'Base directory Web in user settings is: {base_dir}')
+    base_dir = os.path.abspath(os.path.expanduser(base_dir))
+    return base_dir
+
+
+def get_base_dir_kernel():
+    user_settings = get_user_settings()
+    base_dir = user_settings.get('baseDirectoryKernel', '.')  # if baseDirectory is not set, use a default value
+    LOGGER.info(f'Base directory Kernel in user settings is: {base_dir}')
+    base_dir = os.path.abspath(os.path.expanduser(base_dir))
+    return base_dir