Update WIPP extension to use new Python API Client

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.formatting.provider": "black"
+}

jupyterlab_wipp/jupyterlab_wipp/__init__.py

@@ -1,4 +1,5 @@
 import json
+import os
 from pathlib import Path
 
 from ._version import __version__
@@ -8,22 +9,17 @@
 with (HERE / "labextension" / "package.json").open() as fid:
     data = json.load(fid)
 
-def _jupyter_labextension_paths():
-    return [{
-        "src": "labextension",
-        "dest": data["name"]
-    }]
 
+def _jupyter_labextension_paths():
+    return [{"src": "labextension", "dest": data["name"]}]
 
 
 from .handlers import setup_handlers
-from .wipp import Wipp
+from wipp_client import Wipp
 
 
 def _jupyter_server_extension_points():
-    return [{
-        "module": "jupyterlab_wipp"
-    }]
+    return [{"module": "jupyterlab_wipp"}]
 
 
 def _load_jupyter_server_extension(server_app):
@@ -34,10 +30,19 @@ def _load_jupyter_server_extension(server_app):
     server_app: jupyterlab.labapp.LabApp
         JupyterLab application instance
     """
+    wipp_ui_url = os.getenv("WIPP_UI_URL") if "WIPP_UI_URL" in os.environ else ""
+
+    server_app.web_app.settings["wipp_urls"] = {
+        "notebooks_ui_url": os.path.join(wipp_ui_url, "notebooks/"),
+        "imagescollections_ui_url": os.path.join(wipp_ui_url, "images-collections/"),
+        "imagescollection_ui_url": os.path.join(wipp_ui_url, "images-collection/"),
+        "csvcollections_ui_url": os.path.join(wipp_ui_url, "csv-collections/"),
+    }
+
     server_app.web_app.settings["wipp"] = Wipp()
     setup_handlers(server_app.web_app)
     server_app.log.info("Registered jupyterlab_wipp extension at URL path /wipp")
 
+
 # For backward compatibility with notebook server - useful for Binder/JupyterHub
 load_jupyter_server_extension = _load_jupyter_server_extension
-

jupyterlab_wipp/jupyterlab_wipp/handlers.py

@@ -1,33 +1,55 @@
+import os
+import json
+import shutil
+import binascii
+import requests
 from jupyter_server.base.handlers import APIHandler
 from jupyter_server.utils import url_path_join
 import tornado
-import json
+
+
+def gen_random_object_id():
+    """
+    Generate random ObjectID in MongoDB format
+    """
+    timestamp = "{0:x}".format(int(time.time()))
+    rest = binascii.b2a_hex(os.urandom(8)).decode("ascii")
+    return timestamp + rest
+
 
 class WippHandler(APIHandler):
     @property
     def wipp(self):
         return self.settings["wipp"]
 
+    @property
+    def urls(self):
+        return self.settings["wipp_urls"]
+
 
 class InfoCheckHandler(WippHandler):
     @tornado.web.authenticated
     def get(self):
         response = self.wipp.check_api_is_live()
         self.finish(json.dumps(response))
 
+
 class WippUiUrls(WippHandler):
     @tornado.web.authenticated
     def get(self):
         """
         GET request handler, returns relevant WIPP UI URLs
         """
-        self.finish(json.dumps({
-            'root': self.wipp.wipp_ui_url,
-            'notebooks': self.wipp.notebooks_ui_url,
-            'imagescollections': self.wipp.imagescollections_ui_url,
-            'imagescollection': self.wipp.imagescollection_ui_url,
-            'csvcollections': self.wipp.csvcollections_ui_url
-        }))
+        self.finish(
+            json.dumps(
+                {
+                    "notebooks": self.urls["notebooks_ui_url"],
+                    "imagescollections": self.urls["imagescollections_ui_url"],
+                    "imagescollection": self.urls["imagescollection_ui_url"],
+                    "csvcollections": self.urls["csvcollections_ui_url"],
+                }
+            )
+        )
 
 
 class WippRegisterNotebook(WippHandler):
@@ -45,34 +67,87 @@ def post(self):
         """
 
         data = json.loads(self.request.body.decode("utf-8"))
-        if all(key in data for key in ("path","name","description")):
+        temp_notebooks_path = (
+            os.getenv("WIPP_NOTEBOOKS_PATH")
+            if "WIPP_NOTEBOOKS_PATH" in os.environ
+            else "/opt/shared/wipp/temp/notebooks"
+        )
+
+        if all(key in data for key in ("path", "name", "description")):
             try:
-                response = self.wipp.register_notebook(data["path"], data["name"], data["description"])
-                self.finish(json.dumps(response))
+                api_route = (
+                    os.getenv("WIPP_API_INTERNAL_URL")
+                    if "WIPP_API_INTERNAL_URL" in os.environ
+                    else "http://wipp-backend:8080/api"
+                )
+                notebooks_api_route = os.path.join(api_route, "notebooks")
+
+                # Append default path
+                notebook_path = os.path.join(os.environ["HOME"], data["path"])
+
+                # Generate random ObjectID for notebook
+                object_id = gen_random_object_id()
+
+                # Create destination folder in WIPP
+                dest_folder = os.path.join(temp_notebooks_path, object_id)
+                if not os.path.exists(dest_folder):
+                    os.makedirs(dest_folder)
+
+                # Copy notebook to destination folder in WIPP
+                dest_path = os.path.join(dest_folder, "notebook.ipynb")
+                shutil.copy(notebook_path, dest_path)
+
+                # Send API request to WIPP to register notebook
+                url = os.path.join(notebooks_api_route, "import")
+                querystring = {
+                    "folderName": object_id,
+                    "name": data["name"],
+                    "description": data["description"],
+                }
+                response = requests.request("POST", url, params=querystring)
+
+                result = {"code": response.status_code}
+                if response.status_code == 200:
+                    response_json = response.json()
+
+                    # Append workflow URL information
+                    response_json["url"] = self.notebooks_ui_url
+
+                    result["info"] = response_json
+                elif response.status_code == 400:
+                    result["error"] = response.text
+
+                self.finish(json.dumps(result))
             except:
                 self.write_error(500)
         else:
             self.write_error(400)
 
+
 class WippImageCollections(WippHandler):
     @tornado.web.authenticated
     def get(self):
         """
         GET request handler, returns an array of WIPP Image Collections
         """
-        
+
         try:
-            response = self.wipp.get_image_collections()
-            self.finish(json.dumps(response))
+            response = [
+                collection.dict(by_alias=True)
+                for collection in self.wipp.get_image_collections()
+            ]
+
+            self.finish(json.dumps(response, default=str))
         except:
             self.write_error(500)
 
+
 class WippImageCollectionsSearch(WippHandler):
     @tornado.web.authenticated
     def post(self):
         """
         POST request handler
-        Returns an array of WIPP Image Collection which have requested string in the name 
+        Returns an array of WIPP Image Collection which have requested string in the name
 
         Input format:
             {
@@ -83,13 +158,16 @@ def post(self):
         data = json.loads(self.request.body.decode("utf-8"))
         if "name" in data.keys():
             try:
-                response = self.wipp.search_image_collections(data["name"])
-                self.finish(json.dumps(response))
+                response = [
+                    collection.dict(by_alias=True)
+                    for collection in self.wipp.search_image_collections(data["name"])
+                ]
+                self.finish(json.dumps(response, default=str))
             except:
                 self.write_error(500)
         else:
             self.write_error(400)
-        
+
 
 class WippCsvCollections(WippHandler):
     @tornado.web.authenticated
@@ -98,17 +176,22 @@ def get(self):
         GET request handler, returns an array of WIPP Csv Collections
         """
         try:
-            response = self.wipp.get_csv_collections()
-            self.finish(json.dumps(response))
+            response = [
+                collection.dict(by_alias=True)
+                for collection in self.wipp.get_csv_collections()
+            ]
+
+            self.finish(json.dumps(response, default=str))
         except:
             self.write(500)
 
+
 class WippCsvCollectionsSearch(WippHandler):
     @tornado.web.authenticated
     def post(self):
         """
         POST request handler
-        Returns an array of WIPP Csv Collection which have requested string in the name 
+        Returns an array of WIPP Csv Collection which have requested string in the name
 
         Input format:
             {
@@ -119,8 +202,11 @@ def post(self):
         data = json.loads(self.request.body.decode("utf-8"))
         if "name" in data.keys():
             try:
-                response = self.wipp.search_csv_collections(data["name"])
-                self.finish(json.dumps(response))
+                response = [
+                    collection.dict(by_alias=True)
+                    for collection in self.wipp.search_csv_collections(data["name"])
+                ]
+                self.finish(json.dumps(response, default=str))
             except:
                 self.write_error(500)
         else:
@@ -129,13 +215,13 @@ def post(self):
 
 def setup_handlers(web_app):
     handlers = [
-        ('/wipp/info', InfoCheckHandler),
-        ('/wipp/ui_urls', WippUiUrls),
-        ('/wipp/register', WippRegisterNotebook),
-        ('/wipp/imageCollections', WippImageCollections),
-        ('/wipp/imageCollections/search', WippImageCollectionsSearch),
-        ('/wipp/csvCollections', WippCsvCollections),
-        ('/wipp/csvCollections/search', WippCsvCollectionsSearch)
+        ("/wipp/info", InfoCheckHandler),
+        ("/wipp/ui_urls", WippUiUrls),
+        ("/wipp/register", WippRegisterNotebook),
+        ("/wipp/imageCollections", WippImageCollections),
+        ("/wipp/imageCollections/search", WippImageCollectionsSearch),
+        ("/wipp/csvCollections", WippCsvCollections),
+        ("/wipp/csvCollections/search", WippCsvCollectionsSearch),
     ]
 
     base_url = web_app.settings["base_url"]