feat: added internal database option to project addition

README.md

@@ -73,27 +73,29 @@ from obiba_opal import OpalClient, HTTPError, Formatter, ImportCSVCommand, TaskS
 
 # if 2-factor auth is enabled, user will be asked for the secret code
 # Personal access token authentication is also supported (and recommended)
-client = OpalClient.buildWithAuthentication(server='https://opal-demo.obiba.org', user='administrator', password='password')
+client = OpalClient.buildWithAuthentication(
+    server="https://opal-demo.obiba.org", user="administrator", password="password"
+)
 
 try:
     # upload a local CSV data file into Opal file system
     fs = FileService(client)
-    fs.upload_file('./data.csv', '/tmp')
+    fs.upload_file("./data.csv", "/tmp")
 
     # import this CSV file into a project
-    task = ImportCSVCommand(client).import_data('/tmp/data.csv', 'CNSIM')
-    status = TaskService(client).wait_task(task['id'])
-    
+    task = ImportCSVCommand(client).import_data("/tmp/data.csv", "CNSIM")
+    status = TaskService(client).wait_task(task["id"])
+
     # clean data file from Opal
-    fs.delete_file('/tmp/data.csv')
+    fs.delete_file("/tmp/data.csv")
 
-    if status == 'SUCCEEDED':
+    if status == "SUCCEEDED":
         dico = DictionaryService(client)
-        table = dico.get_table('CNSIM', 'data')
+        table = dico.get_table("CNSIM", "data")
         # do something ...
-        dico.delete_tables('CNSIM', ['data'])
+        dico.delete_tables("CNSIM", ["data"])
     else:
-        print('Import failed!')
+        print("Import failed!")
         # do something ...
 except HTTPError as e:
     Formatter.print_json(e.error, True)

obiba_opal/commands.py

@@ -134,12 +134,21 @@ def project_command(
         None, "--name", "-n", help="Project name. Not specifying the project name, will get the list of the projects."
     ),
     database: str | None = typer.Option(
-        None, "--database", "-db", help="Project database name. If not provided only views can be added."
+        None,
+        "--database",
+        "-db",
+        help="Project database name. If not provided and internal is False, only views can be added.",
     ),
     title: str | None = typer.Option(None, "--title", "-t", help="Project title."),
     description: str | None = typer.Option(None, "--description", "-dc", help="Project description."),
     tags: list[str] | None = typer.Option(None, "--tags", "-tg", help="Tags to apply to the project."),
     export_folder: str | None = typer.Option(None, "--export-folder", "-ex", help="Project preferred export folder."),
+    internal: bool = typer.Option(
+        False,
+        "--internal",
+        "-i",
+        help="Create the project using an internal database. Ignored if database is provided.",
+    ),
     add: bool = typer.Option(False, "--add", "-a", help="Add a project (requires at least a project name)."),
     delete: bool = typer.Option(False, "--delete", "-de", help="Delete a project (requires at least a project name)."),
     force: bool = typer.Option(False, "--force", "-f", help="Skip confirmation on project deletion"),
@@ -162,6 +171,7 @@ def project_command(
         description=description,
         tags=tags,
         export_folder=export_folder,
+        internal=internal,
         add=add,
         delete=delete,
         force=force,

obiba_opal/file.py

@@ -119,7 +119,15 @@ def download_file(self, path: str, fd: int | os.PathLike, download_password: str
                 bundle_request = self.client.new_request().fail_on_error()
                 if self.verbose:
                     bundle_request.verbose()
-                response = bundle_request.post().resource("/shell/commands/_file-bundle").accept_json().content_type_json().content(json.dumps(options)).send()
+                response = (
+                    bundle_request
+                    .post()
+                    .resource("/shell/commands/_file-bundle")
+                    .accept_json()
+                    .content_type_json()
+                    .content(json.dumps(options))
+                    .send()
+                )
                 task = response.from_json()
                 task_service = TaskService(self.client)
                 try:
@@ -210,9 +218,7 @@ def get_ws(self):
             return f"/files{self.path}"
 
         def make_bundle_options(self, download_password):
-            options = {
-                "paths": [self.path]
-            }
+            options = {"paths": [self.path]}
             if download_password:
                 options["password"] = download_password
             return options

obiba_opal/project.py

@@ -32,7 +32,7 @@ def add_arguments(cls, parser):
             "--database",
             "-db",
             required=False,
-            help="Project database name. If not provided only views can be added.",
+            help="Project database name. If not provided and internal is False, only views can be added.",
         )
         parser.add_argument("--title", "-t", required=False, help="Project title.")
         parser.add_argument("--description", "-dc", required=False, help="Project description.")
@@ -49,7 +49,12 @@ def add_arguments(cls, parser):
             required=False,
             help="Project preferred export folder.",
         )
-
+        parser.add_argument(
+            "--internal",
+            "-i",
+            action="store_true",
+            help="Create the project using an internal database. Ignored if database is provided.",
+        )
         parser.add_argument(
             "--add",
             "-a",
@@ -94,6 +99,7 @@ def do_command(cls, args):
                 args.description,
                 args.tags,
                 args.export_folder,
+                args.internal,
             )
         elif args.delete:
             if not args.name:
@@ -154,17 +160,22 @@ def add_project(
         description: str = None,
         tags: list = None,
         export_folder: str = None,
+        internal: bool = False,
     ):
         """
         Add a project.
 
         :param name: The project name
-        :param database: The project database name. If not provided only views can be added. See
-            get_databases() for the list of databases available for storage.
+        :param database: The project database name. If not provided and internal is False,
+            only views can be added. See get_databases() for the list of databases available
+            for storage.
         :param title: The project title
         :param description: The project description
         :param tags: The list of project tags
         :param export_folder: The project's preferred export folder
+        :param internal: If True, the project will be created using an internal database. Ignored
+            if database is provided. If False, the project will be created without a database. Default
+            is False.
         """
         if not name:
             raise ValueError("The project name is required.")
@@ -173,6 +184,8 @@ def add_project(
         project = {"name": name}
         if database:
             project["database"] = database
+        elif internal:
+            project["internalDatabase"] = True
         if title:
             project["title"] = title
         else:

obiba_opal/system.py

@@ -453,7 +453,7 @@ def cancel_task(self, id: str | int):
         request.put().resource(f"/shell/command/{id}/status").send()
 
     def wait_task(self, id: str | int, silently: bool = False):
-        """ Wait for the task to complete or being canceled, and return its status. """
+        """Wait for the task to complete or be canceled, and return its status."""
         task = self.get_task(id)
         while task["status"] not in ["SUCCEEDED", "CANCELED", "FAILED", "CANCEL_PENDING"]:
             if not silently:

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "obiba-opal"
-version = "6.1.0"
+version = "6.2.0"
 description = "OBiBa/Opal python client."
 authors = [
     {name = "Yannick Marcon", email = "yannick.marcon@obiba.org"}