vantage6 5.0.0a34__tar.gz → 5.0.0a35__tar.gz

{vantage6-5.0.0a34 → vantage6-5.0.0a35}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vantage6
-Version: 5.0.0a34
+Version: 5.0.0a35
 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==1.10.0
 Requires-Dist: rich==13.5.2
 Requires-Dist: schema==0.7.5
 Requires-Dist: sqlalchemy==2.0.37
-Requires-Dist: vantage6-client==5.0.0a34
-Requires-Dist: vantage6-common==5.0.0a34
+Requires-Dist: vantage6-client==5.0.0a35
+Requires-Dist: vantage6-common==5.0.0a35
 Provides-Extra: dev
 Requires-Dist: black; extra == 'dev'
 Requires-Dist: coverage==7.10.2; extra == 'dev'

{vantage6-5.0.0a34 → vantage6-5.0.0a35}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vantage6"
-version = "5.0.0a34"
+version = "5.0.0a35"
 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==5.0.0a34",
-    "vantage6-client==5.0.0a34",
+    "vantage6-common==5.0.0a35",
+    "vantage6-client==5.0.0a35",
 ]
 
 [project.optional-dependencies]

{vantage6-5.0.0a34 → vantage6-5.0.0a35}/tests_cli/test_node_cli.py

@@ -1,28 +1,27 @@
-import unittest
+import contextlib
 import logging
 import os
-import contextlib
-
-from unittest.mock import MagicMock, patch
-from pathlib import Path
+import unittest
 from io import BytesIO, StringIO
+from pathlib import Path
+from unittest.mock import MagicMock, patch
+
 from click.testing import CliRunner
-from docker.errors import APIError
 
-from vantage6.common.globals import Ports
-from vantage6.cli.globals import APPNAME
 from vantage6.common import STRING_ENCODING
+from vantage6.common.globals import Ports
+
 from vantage6.cli.common.utils import print_log_worker
+from vantage6.cli.globals import APPNAME
+from vantage6.cli.node.attach import cli_node_attach
+from vantage6.cli.node.common import create_client_and_authenticate
+from vantage6.cli.node.create_private_key import cli_node_create_private_key
+from vantage6.cli.node.files import cli_node_files
 from vantage6.cli.node.list import cli_node_list
 from vantage6.cli.node.new import cli_node_new_configuration
-from vantage6.cli.node.files import cli_node_files
-from vantage6.cli.node.start import cli_node_start
 from vantage6.cli.node.restart import cli_node_restart
+from vantage6.cli.node.start import cli_node_start
 from vantage6.cli.node.stop import cli_node_stop
-from vantage6.cli.node.attach import cli_node_attach
-from vantage6.cli.node.create_private_key import cli_node_create_private_key
-from vantage6.cli.node.clean import cli_node_clean
-from vantage6.cli.node.common import create_client_and_authenticate
 
 
 class NodeCLITest(unittest.TestCase):
@@ -302,25 +301,6 @@ class NodeCLITest(unittest.TestCase):
         runner.invoke(cli_node_attach)
         attach_logs.assert_called_once_with("app=node")
 
-    @patch("vantage6.cli.node.clean.q")
-    @patch("docker.DockerClient.volumes")
-    @patch("vantage6.cli.node.clean.check_docker_running", return_value=True)
-    def test_clean(self, check_docker, volumes, q):
-        """Clean Docker volumes without errors."""
-        volume1 = MagicMock()
-        volume1.name = "some-name-tmpvol"
-        volumes.list.return_value = [volume1]
-
-        question = MagicMock(name="pop-the-question")
-        question.ask.return_value = True
-        q.confirm.return_value = question
-
-        runner = CliRunner()
-        result = runner.invoke(cli_node_clean)
-
-        # check exit code
-        self.assertEqual(result.exit_code, 0)
-
     @patch("vantage6.cli.node.create_private_key.create_client_and_authenticate")
     @patch("vantage6.cli.node.common.NodeContext")
     @patch("vantage6.cli.node.create_private_key.NodeContext")
@@ -387,24 +367,6 @@ class NodeCLITest(unittest.TestCase):
 
         self.assertEqual(result.exit_code, 1)
 
-    @patch("vantage6.cli.node.clean.q")
-    @patch("docker.DockerClient.volumes")
-    @patch("vantage6.common.docker.addons.check_docker_running")
-    def test_clean_docker_error(self, check_docker, volumes, q):
-        volume1 = MagicMock()
-        volume1.name = "some-name-tmpvol"
-        volume1.remove.side_effect = APIError("Testing")
-        volumes.list.return_value = [volume1]
-        question = MagicMock(name="pop-the-question")
-        question.ask.return_value = True
-        q.confirm.return_value = question
-
-        runner = CliRunner()
-        result = runner.invoke(cli_node_clean)
-
-        # check exit code
-        self.assertEqual(result.exit_code, 1)
-
     def test_print_log_worker(self):
         stream = BytesIO("Hello!".encode(STRING_ENCODING))
         temp_stdout = StringIO()

vantage6-5.0.0a35/vantage6/cli/algostore/new.py

@@ -0,0 +1,120 @@
+import click
+import questionary as q
+
+from vantage6.common.globals import (
+    DEFAULT_API_PATH,
+    InstanceType,
+    Ports,
+)
+
+from vantage6.cli.common.new import new
+from vantage6.cli.configuration_wizard import add_common_server_config
+from vantage6.cli.globals import DEFAULT_SERVER_SYSTEM_FOLDERS
+
+
+@click.command()
+@click.option(
+    "-n", "--name", default=None, help="Name of the configuration you want to use."
+)
+@click.option(
+    "--system",
+    "system_folders",
+    flag_value=True,
+    help="Use system folders instead of user folders. This is the default",
+)
+@click.option(
+    "--user",
+    "system_folders",
+    flag_value=False,
+    default=DEFAULT_SERVER_SYSTEM_FOLDERS,
+    help="Use user folders instead of system folders",
+)
+@click.option("--context", default=None, help="Kubernetes context to use")
+@click.option(
+    "--namespace",
+    default=None,
+    help="Kubernetes namespace to use",
+)
+def cli_algo_store_new(
+    name: str, system_folders: bool, namespace: str, context: str
+) -> None:
+    """
+    Create a new server configuration.
+    """
+
+    new(
+        questionnaire_function=algo_store_configuration_questionaire,
+        name=name,
+        system_folders=system_folders,
+        namespace=namespace,
+        context=context,
+        type_=InstanceType.ALGORITHM_STORE,
+    )
+
+
+def algo_store_configuration_questionaire(instance_name: str) -> dict:
+    """
+    Questionary to generate a config file for the algorithm store server
+    instance.
+
+    Parameters
+    ----------
+    instance_name : str
+        Name of the server instance.
+
+    Returns
+    -------
+    dict
+        Dictionary with the new server configuration
+    """
+    config = {"store": {}, "database": {}}
+
+    config, is_production = add_common_server_config(
+        config, InstanceType.ALGORITHM_STORE, instance_name
+    )
+    if not is_production:
+        config["store"]["dev"] = {
+            "host_uri": "host.docker.internal",
+            "disable_review": True,
+            "review_own_algorithm": True,
+        }
+
+    default_v6_server_uri = f"http://localhost:{Ports.DEV_SERVER}{DEFAULT_API_PATH}"
+    default_root_username = "admin"
+
+    v6_server_uri = q.text(
+        "What is the Vantage6 server linked to the algorithm store? "
+        "Provide the link to the server endpoint.",
+        default=default_v6_server_uri,
+    ).unsafe_ask()
+
+    root_username = q.text(
+        "What is the username of the root user?",
+        default=default_root_username,
+    ).unsafe_ask()
+
+    config["root_user"] = {
+        "v6_server_uri": v6_server_uri,
+        "username": root_username,
+    }
+
+    # ask about openness of the algorithm store
+    config["policies"] = {}
+    is_open = q.confirm(
+        "Do you want to open the algorithm store to the public? This will allow anyone "
+        "to view the algorithms, but they cannot modify them.",
+        default=False,
+    ).unsafe_ask()
+    if is_open:
+        open_algos_policy = "public"
+    else:
+        is_open_to_whitelist = q.confirm(
+            "Do you want to allow all authenticated users to access "
+            "the algorithms in the store? If not allowing this, you will have to assign"
+            " the appropriate permissions to each user individually.",
+            default=True,
+        ).unsafe_ask()
+        open_algos_policy = "authenticated" if is_open_to_whitelist else "private"
+    config["policies"]["algorithm_view"] = open_algos_policy
+
+    return config

vantage6-5.0.0a35/vantage6/cli/algostore/remove.py

@@ -0,0 +1,36 @@
+import click
+
+from vantage6.common.globals import InstanceType
+
+from vantage6.cli.common.decorator import click_insert_context
+from vantage6.cli.common.remove import execute_remove
+from vantage6.cli.context import AlgorithmStoreContext
+from vantage6.cli.globals import InfraComponentName
+
+
+@click.command()
+@click_insert_context(
+    type_=InstanceType.ALGORITHM_STORE, include_name=True, include_system_folders=True
+)
+@click.option("-f", "--force", "force", flag_value=True)
+def cli_algo_store_remove(
+    ctx: AlgorithmStoreContext, name: str, system_folders: bool, force: bool
+) -> None:
+    """
+    Function to remove an algorithm store.
+
+    Parameters
+    ----------
+    ctx : AlgorithmStoreContext
+        Algorithm store context object
+    force : bool
+        Whether to ask for confirmation before removing or not
+    """
+    execute_remove(
+        ctx,
+        InstanceType.ALGORITHM_STORE,
+        InfraComponentName.ALGORITHM_STORE,
+        name,
+        system_folders,
+        force,
+    )

{vantage6-5.0.0a34 → vantage6-5.0.0a35}/vantage6/cli/algostore/start.py

@@ -9,12 +9,12 @@ from vantage6.common.globals import (
 from vantage6.cli.common.decorator import click_insert_context
 from vantage6.cli.common.start import (
     helm_install,
+    prestart_checks,
     start_port_forward,
 )
 from vantage6.cli.common.utils import (
     attach_logs,
     create_directory_if_not_exists,
-    select_context_and_namespace,
 )
 from vantage6.cli.context.algorithm_store import AlgorithmStoreContext
 from vantage6.cli.globals import ChartName
@@ -30,9 +30,13 @@ from vantage6.cli.globals import ChartName
     default=False,
     help="Print server logs to the console after start",
 )
-@click_insert_context(InstanceType.ALGORITHM_STORE)
+@click_insert_context(
+    InstanceType.ALGORITHM_STORE, include_name=True, include_system_folders=True
+)
 def cli_algo_store_start(
     ctx: AlgorithmStoreContext,
+    name: str,
+    system_folders: bool,
     context: str,
     namespace: str,
     ip: str,
@@ -43,9 +47,9 @@ def cli_algo_store_start(
     Start the algorithm store.
     """
     info("Starting algorithm store...")
-    context, namespace = select_context_and_namespace(
-        context=context,
-        namespace=namespace,
+
+    prestart_checks(
+        ctx, InstanceType.ALGORITHM_STORE, name, system_folders, context, namespace
     )
 
     create_directory_if_not_exists(ctx.log_dir)
@@ -58,10 +62,9 @@ def cli_algo_store_start(
         namespace=namespace,
     )
 
-    # port forward for server
     info("Port forwarding for algorithm store")
     start_port_forward(
-        service_name=f"{ctx.helm_release_name}-vantage6-algorithm-store-service",
+        service_name=f"{ctx.helm_release_name}-store-service",
         service_port=ctx.config["store"].get("port", Ports.DEV_ALGO_STORE.value),
         port=port or ctx.config["store"].get("port", Ports.DEV_ALGO_STORE.value),
         ip=ip,

vantage6-5.0.0a35/vantage6/cli/algostore/stop.py

@@ -0,0 +1,58 @@
+import click
+
+from vantage6.common import info
+from vantage6.common.globals import InstanceType
+
+from vantage6.cli.common.stop import execute_stop, helm_uninstall, stop_port_forward
+from vantage6.cli.globals import DEFAULT_SERVER_SYSTEM_FOLDERS, InfraComponentName
+
+
+@click.command()
+@click.option("-n", "--name", default=None, help="Configuration name")
+@click.option("--context", default=None, help="Kubernetes context to use")
+@click.option("--namespace", default=None, help="Kubernetes namespace to use")
+@click.option(
+    "--system",
+    "system_folders",
+    flag_value=True,
+    default=DEFAULT_SERVER_SYSTEM_FOLDERS,
+    help="Search for configuration in system folders instead of user folders. "
+    "This is the default.",
+)
+@click.option(
+    "--user",
+    "system_folders",
+    flag_value=False,
+    help="Search for configuration in the user folders instead of system folders.",
+)
+@click.option("--all", "all_stores", flag_value=True, help="Stop all algorithm stores")
+def cli_algo_store_stop(
+    name: str,
+    context: str,
+    namespace: str,
+    system_folders: bool,
+    all_stores: bool,
+):
+    """
+    Stop one or all running algorithm store(s).
+    """
+    execute_stop(
+        stop_function=_stop_store,
+        instance_type=InstanceType.ALGORITHM_STORE,
+        infra_component=InfraComponentName.ALGORITHM_STORE,
+        stop_all=all_stores,
+        to_stop=name,
+        namespace=namespace,
+        context=context,
+        system_folders=system_folders,
+    )
+
+
+def _stop_store(store_name: str, namespace: str, context: str) -> None:
+    info(f"Stopping store {store_name}...")
+
+    helm_uninstall(release_name=store_name, context=context, namespace=namespace)
+
+    stop_port_forward(service_name=f"{store_name}-store-service")
+
+    info(f"Store {store_name} stopped successfully.")

{vantage6-5.0.0a34 → vantage6-5.0.0a35}/vantage6/cli/cli.py

@@ -1,17 +1,19 @@
 import click
 
-from vantage6.cli.server.attach import cli_server_attach
-from vantage6.cli.server.files import cli_server_files
-from vantage6.cli.server.import_ import cli_server_import
-from vantage6.cli.server.list import cli_server_configuration_list
-from vantage6.cli.server.new import cli_server_new
-from vantage6.cli.server.remove import cli_server_remove
-from vantage6.cli.server.shell import cli_server_shell
-from vantage6.cli.server.start import cli_server_start
-from vantage6.cli.server.stop import cli_server_stop
-from vantage6.cli.server.version import cli_server_version
+from vantage6.cli.algorithm.create import cli_algorithm_create
+from vantage6.cli.algorithm.generate_algorithm_json import (
+    cli_algorithm_generate_algorithm_json,
+)
+from vantage6.cli.algorithm.update import cli_algorithm_update
+from vantage6.cli.algostore.attach import cli_algo_store_attach
+from vantage6.cli.algostore.files import cli_algo_store_files
+from vantage6.cli.algostore.list import cli_algo_store_configuration_list
+from vantage6.cli.algostore.new import cli_algo_store_new
+from vantage6.cli.algostore.remove import cli_algo_store_remove
+from vantage6.cli.algostore.start import cli_algo_store_start
+from vantage6.cli.algostore.stop import cli_algo_store_stop
+from vantage6.cli.globals import CLICommandName
 from vantage6.cli.node.attach import cli_node_attach
-from vantage6.cli.node.clean import cli_node_clean
 from vantage6.cli.node.create_private_key import cli_node_create_private_key
 from vantage6.cli.node.files import cli_node_files
 from vantage6.cli.node.list import cli_node_list
@@ -22,29 +24,26 @@ from vantage6.cli.node.set_api_key import cli_node_set_api_key
 from vantage6.cli.node.start import cli_node_start
 from vantage6.cli.node.stop import cli_node_stop
 from vantage6.cli.node.version import cli_node_version
-from vantage6.cli.algorithm.create import cli_algorithm_create
-from vantage6.cli.algorithm.update import cli_algorithm_update
-from vantage6.cli.algorithm.generate_algorithm_json import (
-    cli_algorithm_generate_algorithm_json,
-)
+from vantage6.cli.server.attach import cli_server_attach
+from vantage6.cli.server.files import cli_server_files
+from vantage6.cli.server.import_ import cli_server_import
+from vantage6.cli.server.list import cli_server_configuration_list
+from vantage6.cli.server.new import cli_server_new
+from vantage6.cli.server.remove import cli_server_remove
+from vantage6.cli.server.shell import cli_server_shell
+from vantage6.cli.server.start import cli_server_start
+from vantage6.cli.server.stop import cli_server_stop
+from vantage6.cli.server.version import cli_server_version
 
 # from vantage6.cli.test.client_script import cli_test_client_script
-from vantage6.cli.test.feature_tester import cli_test_features
-
 # from vantage6.cli.test.integration_test import cli_test_integration
-from vantage6.cli.algostore.attach import cli_algo_store_attach
-from vantage6.cli.algostore.new import cli_algo_store_new
-from vantage6.cli.algostore.start import cli_algo_store_start
-from vantage6.cli.algostore.stop import cli_algo_store_stop
-from vantage6.cli.algostore.files import cli_algo_store_files
-from vantage6.cli.algostore.list import cli_algo_store_configuration_list
-from vantage6.cli.algostore.remove import cli_algo_store_remove
+from vantage6.cli.test.feature_tester import cli_test_features
 from vantage6.cli.use.context import cli_use_context
 from vantage6.cli.use.namespace import cli_use_namespace
 
 
 # Define the server group
-@click.group(name="server")
+@click.group(name=CLICommandName.SERVER.value)
 def cli_server() -> None:
     """
     Manage your vantage6 server instances.
@@ -65,7 +64,7 @@ cli_server.add_command(cli_server_version, name="version")
 
 
 # Define the node group
-@click.group(name="node")
+@click.group(name=CLICommandName.NODE.value)
 def cli_node() -> None:
     """
     Manage your vantage6 node instances.
@@ -74,7 +73,6 @@ def cli_node() -> None:
 
 # Define the commands for the node group
 cli_node.add_command(cli_node_attach, name="attach")
-cli_node.add_command(cli_node_clean, name="clean")
 cli_node.add_command(cli_node_create_private_key, name="create-private-key")
 cli_node.add_command(cli_node_files, name="files")
 cli_node.add_command(cli_node_list, name="list")
@@ -88,7 +86,7 @@ cli_node.add_command(cli_node_version, name="version")
 
 
 # Define the dev group
-@click.group(name="dev")
+@click.group(name=CLICommandName.DEV.value)
 def cli_dev() -> None:
     """
     Quickly manage a test network with a server and several nodes.
@@ -101,7 +99,7 @@ def cli_dev() -> None:
 
 
 # Define the algorithm group
-@click.group(name="algorithm")
+@click.group(name=CLICommandName.ALGORITHM.value)
 def cli_algorithm() -> None:
     """
     Manage your vantage6 algorithms.
@@ -117,7 +115,7 @@ cli_algorithm.add_command(
 
 
 # Define the test group
-@click.group(name="test")
+@click.group(name=CLICommandName.TEST.value)
 def cli_test() -> None:
     """
     Execute tests on your vantage6 infrastructure.
@@ -131,7 +129,7 @@ cli_test.add_command(cli_test_features, name="feature-test")
 
 
 # Define the algorithm-store group
-@click.group(name="algorithm-store")
+@click.group(name=CLICommandName.ALGORITHM_STORE.value)
 def cli_algo_store() -> None:
     """
     Manage your vantage6 algorithm store server instances.
@@ -149,7 +147,7 @@ cli_algo_store.add_command(cli_algo_store_remove, name="remove")
 
 
 # Add the use group
-@click.group(name="use")
+@click.group(name=CLICommandName.USE.value)
 def cli_use() -> None:
     """
     Manage Kubernetes context and namespace.

{vantage6-5.0.0a34 → vantage6-5.0.0a35}/vantage6/cli/common/new.py

@@ -11,8 +11,31 @@ from vantage6.cli.utils import check_config_name_allowed, prompt_config_name
 
 
 def new(
-    name: str, system_folders: bool, namespace: str, context: str, type_: InstanceType
-):
+    questionnaire_function: callable,
+    name: str,
+    system_folders: bool,
+    namespace: str,
+    context: str,
+    type_: InstanceType,
+) -> None:
+    """
+    Create a new configuration.
+
+    Parameters
+    ----------
+    questionnaire_function : callable
+        Function to generate the configuration
+    name : str
+        Name of the configuration
+    system_folders : bool
+        Whether to store the configuration in the system folders
+    namespace : str
+        Namespace to use
+    context : str
+        Context to use
+    type_ : InstanceType
+        Type of the configuration (node, server, algorithm store, etc)
+    """
     cli_config = CliConfig()
     context, namespace = cli_config.compare_changes_config(
         context=context,
@@ -47,7 +70,9 @@ def new(
 
     # create config in ctx location
     try:
-        cfg_file = configuration_wizard(type_, name, system_folders)
+        cfg_file = configuration_wizard(
+            questionnaire_function, type_, name, system_folders
+        )
     except KeyboardInterrupt:
         error("Configuration creation aborted.")
         exit(1)

vantage6-5.0.0a35/vantage6/cli/common/remove.py

@@ -0,0 +1,54 @@
+import itertools
+from pathlib import Path
+from shutil import rmtree
+
+import questionary as q
+
+from vantage6.common import (
+    error,
+    info,
+)
+from vantage6.common.context import AppContext
+from vantage6.common.globals import InstanceType
+
+from vantage6.cli.common.utils import check_running
+from vantage6.cli.globals import InfraComponentName
+from vantage6.cli.utils import remove_file
+
+
+def execute_remove(
+    ctx: AppContext,
+    instance_type: InstanceType,
+    infra_component: InfraComponentName,
+    name: str,
+    system_folders: bool,
+    force: bool,
+) -> None:
+    if check_running(ctx.helm_release_name, instance_type, name, system_folders):
+        error(
+            f"The {infra_component.value} {name} is still running! Please stop the "
+            f"{infra_component.value} before deleting it."
+        )
+        exit(1)
+
+    if not force:
+        if not q.confirm(
+            f"This {infra_component.value} will be deleted permanently including its "
+            "configuration. Are you sure?",
+            default=False,
+        ).ask():
+            info(f"The {infra_component.value} {name} will not be deleted")
+            exit(0)
+
+    # remove the config file
+    remove_file(ctx.config_file, "configuration")
+
+    # ensure log files are closed before removing
+    log_dir = Path(ctx.log_file.parent)
+    if log_dir.exists():
+        info(f"Removing log directory: {log_dir}")
+        for handler in itertools.chain(ctx.log.handlers, ctx.log.root.handlers):
+            handler.close()
+        # remove the whole folder with all the log files. This may also still contain
+        # other files like (for the server) RabbitMQ configuration etc
+        rmtree(log_dir)

{vantage6-5.0.0a34 → vantage6-5.0.0a35}/vantage6/cli/common/start.py

@@ -10,6 +10,7 @@ import docker
 from docker.client import DockerClient
 
 from vantage6.common import error, info, warning
+from vantage6.common.context import AppContext
 from vantage6.common.docker.addons import pull_image
 from vantage6.common.globals import (
     DEFAULT_ALGO_STORE_IMAGE,
@@ -21,8 +22,36 @@ from vantage6.common.globals import (
     InstanceType,
 )
 
+from vantage6.cli.common.utils import (
+    check_running,
+    select_context_and_namespace,
+)
 from vantage6.cli.globals import ChartName
-from vantage6.cli.utils import validate_input_cmd_args
+from vantage6.cli.utils import check_config_name_allowed, validate_input_cmd_args
+
+
+def prestart_checks(
+    ctx: AppContext,
+    instance_type: InstanceType,
+    name: str,
+    system_folders: bool,
+    context: str,
+    namespace: str,
+) -> None:
+    """
+    Run pre-start checks for an instance.
+    """
+
+    check_config_name_allowed(ctx.name)
+
+    if check_running(ctx.helm_release_name, instance_type, name, system_folders):
+        error(f"Instance '{name}' is already running.")
+        exit(1)
+
+    context, namespace = select_context_and_namespace(
+        context=context,
+        namespace=namespace,
+    )
 
 
 def pull_infra_image(