vantage6 5.0.0a38__tar.gz → 5.0.0a41__tar.gz

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vantage6
-Version: 5.0.0a38
+Version: 5.0.0a41
 Summary: vantage6 command line interface
 Author: Vantage6 Team
 Maintainer-email: Frank Martin <f.martin@iknl.nl>, Bart van Beusekom <b.vanbeusekom@iknl.nl>
@@ -18,8 +18,8 @@ Requires-Dist: questionary==2.1.1
 Requires-Dist: rich==13.5.2
 Requires-Dist: schema==0.7.5
 Requires-Dist: sqlalchemy==2.0.37
-Requires-Dist: vantage6-client==5.0.0a38
-Requires-Dist: vantage6-common==5.0.0a38
+Requires-Dist: vantage6-client==5.0.0a41
+Requires-Dist: vantage6-common==5.0.0a41
 Provides-Extra: dev
 Requires-Dist: black; extra == 'dev'
 Requires-Dist: coverage==7.10.2; extra == 'dev'

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vantage6"
-version = "5.0.0a38"
+version = "5.0.0a41"
 description = "vantage6 command line interface"
 readme = "README.md"
 license = {text = "MIT"}
@@ -29,8 +29,8 @@ dependencies = [
     "rich==13.5.2",
     "schema==0.7.5",
     "sqlalchemy==2.0.37",
-    "vantage6-common==5.0.0a38",
-    "vantage6-client==5.0.0a38",
+    "vantage6-common==5.0.0a41",
+    "vantage6-client==5.0.0a41",
 ]
 
 [project.optional-dependencies]

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/vantage6/cli/algorithm/generate_algorithm_json.py

@@ -3,6 +3,7 @@ import inspect
 import json
 import os
 import sys
+from collections.abc import Callable
 from inspect import getmembers, isfunction, ismodule, signature
 from pathlib import Path
 from types import ModuleType, UnionType
@@ -62,7 +63,7 @@ class FunctionArgumentType(StrEnumBase):
 class Function:
     """Class to handle a function and its JSON representation"""
 
-    def __init__(self, func: callable):
+    def __init__(self, func: Callable):
         self.func = func
         self.name = func.__name__
         self.signature = signature(func)

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/vantage6/cli/common/decorator.py

@@ -1,3 +1,4 @@
+from collections.abc import Callable
 from functools import wraps
 from pathlib import Path
 
@@ -17,7 +18,7 @@ def click_insert_context(
     include_system_folders: bool = False,
     is_sandbox: bool = False,
     sandbox_param: str | None = None,
-) -> callable:
+) -> Callable:
     """
     Supply the Click function with an additional context parameter. The context
     is passed to the function as the first argument.
@@ -49,7 +50,7 @@ def click_insert_context(
     >>>     pass
     """
 
-    def protection_decorator(func: callable) -> callable:
+    def protection_decorator(func: Callable) -> Callable:
         @click.option("-n", "--name", default=None, help="Name of the configuration.")
         @click.option(
             "-c",
@@ -73,7 +74,7 @@ def click_insert_context(
         @wraps(func)
         def decorator(
             name: str, config: str, system_folders: bool, *args, **kwargs
-        ) -> callable:
+        ) -> Callable:
             """
             Decorator function that adds the context to the function.
 

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/vantage6/cli/common/new.py

@@ -1,3 +1,4 @@
+from collections.abc import Callable
 from pathlib import Path
 
 from colorama import Fore, Style
@@ -13,7 +14,7 @@ from vantage6.cli.utils import check_config_name_allowed, prompt_config_name
 
 
 def new(
-    config_producing_func: callable,
+    config_producing_func: Callable,
     config_producing_func_args: tuple,
     name: str,
     system_folders: bool,
@@ -27,7 +28,7 @@ def new(
 
     Parameters
     ----------
-    config_producing_func : callable
+    config_producing_func : Callable
         Function to generate the configuration
     config_producing_func_args : tuple
         Arguments to pass to the config producing function

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/vantage6/cli/common/stop.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import subprocess
+from collections.abc import Callable
 
 from colorama import Fore, Style
 
@@ -19,7 +20,7 @@ from vantage6.cli.utils import validate_input_cmd_args
 
 
 def execute_stop(
-    stop_function: callable,
+    stop_function: Callable,
     instance_type: InstanceType,
     infra_component: InfraComponentName,
     stop_all: bool,
@@ -35,7 +36,7 @@ def execute_stop(
 
     Parameters
     ----------
-    stop_function : callable
+    stop_function : Callable
         The function to stop the service.
     instance_type : InstanceType
         The instance type of the service.

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/vantage6/cli/configuration_create.py

@@ -1,3 +1,4 @@
+from collections.abc import Callable
 from pathlib import Path
 
 import questionary as q
@@ -127,7 +128,7 @@ def _add_production_server_config(config: dict) -> dict:
 
 
 def make_configuration(
-    config_producing_func: callable,
+    config_producing_func: Callable,
     config_producing_func_args: tuple,
     type_: InstanceType,
     instance_name: str,
@@ -139,7 +140,7 @@ def make_configuration(
 
     Parameters
     ----------
-    config_producing_func : callable
+    config_producing_func : Callable
         Function to generate the configuration
     config_producing_func_args : tuple
         Arguments to pass to the config producing function

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/vantage6/cli/node/common/__init__.py

@@ -12,6 +12,7 @@ from vantage6.common.globals import (
     APPNAME,
     HTTP_LOCALHOST,
     InstanceType,
+    Ports,
     RequiredNodeEnvVars,
 )
 
@@ -21,6 +22,16 @@ from vantage6.cli.configuration_create import select_configuration_questionnaire
 from vantage6.cli.context.node import NodeContext
 
 
+def _convert_k8s_url_to_localhost(url: str) -> str:
+    """
+    Convert a Kubernetes URL to a localhost URL.
+    """
+    if "svc.cluster.local" in url:
+        port_and_api_path = url.split(":")[-1]
+        return f"{HTTP_LOCALHOST}:{port_and_api_path}"
+    return url
+
+
 def create_client(ctx: NodeContext) -> UserClient:
     """
     Create a client instance.
@@ -34,17 +45,31 @@ def create_client(ctx: NodeContext) -> UserClient:
     UserClient
         vantage6 client
     """
-    host = ctx.config["server_url"]
+    host = ctx.config["node"]["server"]["url"]
+    port = ctx.config["node"]["server"]["port"]
+    api_path = ctx.config["node"]["server"]["path"]
     # if the server is run locally, we need to use localhost here instead of
     # the host address of docker
     if host in ["http://host.docker.internal", "http://172.17.0.1"]:
         host = HTTP_LOCALHOST
-    port = ctx.config["port"]
-    api_path = ctx.config["api_path"]
-    info(f"Connecting to server at '{host}:{port}{api_path}'")
+
+    url = f"{host}:{port}{api_path}"
+
+    auth_url = ctx.config.get("node", {}).get("keycloakUrl", None) or os.environ.get(
+        RequiredNodeEnvVars.KEYCLOAK_URL.value
+    )
+    # append the port to the auth URL as it is not included in the config
+    auth_url = f"{auth_url}:{Ports.DEV_AUTH.value}"
+
+    # if the server is a Kubernetes address, we need to use localhost because here
+    # we are connecting from the CLI outside the cluster
+    url = _convert_k8s_url_to_localhost(url)
+    auth_url = _convert_k8s_url_to_localhost(auth_url)
+
+    info(f"Connecting to server at '{url}' using auth URL '{auth_url}'")
     return UserClient(
-        server_url=f"{host}:{port}{api_path}",
-        auth_url=os.environ.get(RequiredNodeEnvVars.KEYCLOAK_URL.value),
+        server_url=url,
+        auth_url=auth_url,
         log_level="warn",
     )
 

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/vantage6/cli/node/create_private_key.py

@@ -11,10 +11,12 @@ from vantage6.common import (
     warning,
 )
 from vantage6.common.encryption import RSACryptor
+from vantage6.common.globals import InstanceType
 
+from vantage6.cli.configuration_create import select_configuration_questionnaire
 from vantage6.cli.context.node import NodeContext
 from vantage6.cli.globals import DEFAULT_NODE_SYSTEM_FOLDERS as N_FOL
-from vantage6.cli.node.common import create_client_and_authenticate, select_node
+from vantage6.cli.node.common import create_client_and_authenticate
 
 
 @click.command()
@@ -80,12 +82,13 @@ def cli_node_create_private_key(
     if config:
         name = Path(config).stem
         ctx = NodeContext(name, system_folders, config)
-    else:
-        # retrieve context
-        name = select_node(name, system_folders)
-
-        # Create node context
-        ctx = NodeContext(name, system_folders)
+    elif not name:
+        try:
+            name = select_configuration_questionnaire(InstanceType.NODE, system_folders)
+        except Exception:
+            error("No configurations could be found!")
+            exit(1)
+    ctx = NodeContext(name, system_folders)
 
     # Authenticate with the server to obtain organization name if it wasn't
     # provided
@@ -138,9 +141,7 @@ def cli_node_create_private_key(
 
     # update config file
     info("Updating configuration")
-    # TODO v5+ this probably messes up the current config as the template is used...
-    # Fix when reimplementing this in v5
-    ctx.config["encryption"]["private_key"] = str(file_)
+    ctx.config["node"]["encryption"]["private_key"] = str(file_)
     ctx.config_manager.put(ctx.config)
     ctx.config_manager.save(ctx.config_file)
 

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/vantage6/cli/node/set_api_key.py

@@ -2,11 +2,14 @@ import click
 import questionary as q
 
 from vantage6.common import ensure_config_dir_writable, error, info
+from vantage6.common.globals import InstanceType
 
-from vantage6.cli.configuration_create import NodeConfigurationManager
+from vantage6.cli.configuration_create import (
+    NodeConfigurationManager,
+    select_configuration_questionnaire,
+)
 from vantage6.cli.context.node import NodeContext
 from vantage6.cli.globals import DEFAULT_NODE_SYSTEM_FOLDERS as N_FOL
-from vantage6.cli.node.common import select_node
 
 
 @click.command()
@@ -31,7 +34,12 @@ def cli_node_set_api_key(name: str, api_key: str, system_folders: bool) -> None:
     Put a new API key into the node configuration file
     """
     # select node name
-    name = select_node(name, system_folders)
+    if not name:
+        try:
+            name = select_configuration_questionnaire(InstanceType.NODE, system_folders)
+        except Exception:
+            error("No configurations could be found!")
+            exit(1)
 
     # Check that we can write in the config folder
     if not ensure_config_dir_writable(system_folders):
@@ -50,9 +58,7 @@ def cli_node_set_api_key(name: str, api_key: str, system_folders: bool) -> None:
     conf_mgr = NodeConfigurationManager.from_file(ctx.config_file)
 
     # set new api key, and save the file
-    ctx.config["api_key"] = api_key
-    # TODO v5+ this probably messes up the current config as the template is used...
-    # Fix when reimplementing this in v5
+    ctx.config["node"]["apiKey"] = api_key
     conf_mgr.put(ctx.config)
     conf_mgr.save(ctx.config_file)
     info(f"Your new API key has been uploaded to the config file {ctx.config_file}.")

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/vantage6/cli/server/import_.py

@@ -1,6 +1,7 @@
 import click
 import requests
 import yaml
+from marshmallow import Schema, ValidationError, fields, post_load
 
 from vantage6.common import error, info
 from vantage6.common.globals import (
@@ -64,7 +65,8 @@ def cli_server_import(ctx: ServerContext, file: str, drop_all: bool) -> None:
     info("Loading and validating import file")
     with open(file, "r") as f:
         import_data = yaml.safe_load(f)
-    # TODO: validate import file
+
+    _check_import_file(import_data)
 
     client = UserClient(
         server_url=f"{ctx.config['server']['baseUrl']}{ctx.config['server']['apiPath']}",
@@ -77,7 +79,9 @@ def cli_server_import(ctx: ServerContext, file: str, drop_all: bool) -> None:
     info("Authenticate using admin credentials (opens browser for login)")
     client.authenticate()
 
-    # TODO: validate that the user has the correct permissions to import data
+    # Note: we do not validate that the user has the correct permissions to import data.
+    # As the user has access to the `v6 server import` command, they already have
+    # access to the server+database.
 
     if drop_all:
         info("Dropping all existing data")
@@ -91,11 +95,12 @@ def cli_server_import(ctx: ServerContext, file: str, drop_all: bool) -> None:
     for organization in import_data["organizations"]:
         org = client.organization.create(
             name=organization["name"],
-            address1=organization["address1"] or "",
-            address2=organization["address2"] or "",
-            zipcode=organization["zipcode"] or "",
-            country=organization["country"] or "",
-            domain=organization["domain"] or "",
+            address1=organization.get("address1", ""),
+            address2=organization.get("address2", ""),
+            zipcode=str(organization.get("zipcode", "")),
+            country=organization.get("country", ""),
+            domain=organization.get("domain", ""),
+            public_key=organization.get("public_key", ""),
         )
         organizations.append(org)
 
@@ -152,16 +157,79 @@ def _drop_all(client: UserClient) -> None:
             info(f"Deleting collaboration {collaboration['name']}")
             client.collaboration.delete(collaboration["id"], delete_dependents=True)
 
-    # TODO: For some reason, the `delete_dependents` parameter is not working for users,
-    # so we delete them here first.
-    while users := [u for u in client.user.list()["data"] if u["username"] != "admin"]:
-        for user in users:
-            info(f"Deleting user {user['username']}")
-            client.user.delete(user["id"])
-
-    while orgs := [
-        o for o in client.organization.list()["data"] if o["name"] != "root"
-    ]:
+    # remove all organizations but keep the root organization
+    while orgs := [o for o in client.organization.list()["data"] if o["id"] != 1]:
         for org in orgs:
             info(f"Deleting organization {org['name']}")
             client.organization.delete(org["id"], delete_dependents=True)
+
+
+class StrOrInt(fields.Field):
+    """Field that can be a string or an integer"""
+
+    def _serialize(self, value, attr, obj, **kwargs):
+        if isinstance(value, str):
+            return value
+        elif isinstance(value, int):
+            return str(value)
+        else:
+            raise ValidationError("Value must be a string or an integer")
+
+
+class UserSchema(Schema):
+    username = fields.Str(required=True)
+    password = fields.Str(required=True)
+
+
+class OrganizationSchema(Schema):
+    name = fields.Str(required=True)
+    address1 = fields.Str(missing="")
+    address2 = fields.Str(missing="")
+    zipcode = StrOrInt(missing="")
+    country = fields.Str(missing="")
+    domain = fields.Str(missing="")
+    public_key = fields.Str(missing="")
+    users = fields.List(fields.Nested(UserSchema), missing=[])
+
+
+class ParticipantSchema(Schema):
+    name = fields.Str(required=True)
+
+
+class CollaborationSchema(Schema):
+    name = fields.Str(required=True)
+    participants = fields.List(fields.Nested(ParticipantSchema), required=True)
+    encrypted = fields.Bool(missing=False)
+
+
+class ImportDataSchema(Schema):
+    organizations = fields.List(fields.Nested(OrganizationSchema), missing=[])
+    collaborations = fields.List(fields.Nested(CollaborationSchema), missing=[])
+
+    @post_load
+    def validate_participants_exist(self, data, **kwargs):
+        """Validate that all participants exist in organizations"""
+        org_names = {org["name"] for org in data.get("organizations", [])}
+
+        for collaboration in data.get("collaborations", []):
+            for participant in collaboration.get("participants", []):
+                if participant["name"] not in org_names:
+                    raise ValidationError(
+                        f"Participant {participant['name']} not found in organizations",
+                        field_name="collaborations",
+                    )
+        return data
+
+
+def _check_import_file(import_data: dict) -> dict:
+    """
+    Validate import file using Marshmallow schemas.
+    Returns the validated and cleaned data.
+    """
+    schema = ImportDataSchema()
+    try:
+        return schema.load(import_data)
+    except ValidationError as err:
+        # Handle validation errors gracefully
+        error(f"Validation error: {err.messages}")
+        exit(1)

{vantage6-5.0.0a38 → vantage6-5.0.0a41}/vantage6/cli/template/node_config.j2

@@ -90,7 +90,7 @@ node:
     enabled: {{ node.encryption.enabled | default(false) }}
 
     # Location to the private key file. Required if encryption is enabled.
-    {% if node.encryption.enabled | default(false) %}
+    {% if node.encryption.private_key is defined and node.encryption.private_key != '' %}
     private_key: {{ node.encryption.private_key | default('/path/to/private_key.pem') }}
     {% else %}
     # private_key: /path/to/private_key.pem