vantage6 4.8.2__py3-none-any.whl → 4.9.0__py3-none-any.whl

tests_cli/test_node_cli.py

@@ -17,6 +17,7 @@ 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.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
@@ -85,7 +86,7 @@ class NodeCLITest(unittest.TestCase):
         )
 
     @patch("vantage6.cli.node.new.configuration_wizard")
-    @patch("vantage6.cli.node.new.check_config_writeable")
+    @patch("vantage6.cli.node.new.ensure_config_dir_writable")
     @patch("vantage6.cli.node.common.NodeContext")
     def test_new_config(self, context, permissions, wizard):
         """No error produced when creating new configuration."""
@@ -147,7 +148,7 @@ class NodeCLITest(unittest.TestCase):
         # check non-zero exit code
         self.assertEqual(result.exit_code, 1)
 
-    @patch("vantage6.cli.node.new.check_config_writeable")
+    @patch("vantage6.cli.node.new.ensure_config_dir_writable")
     @patch("vantage6.cli.node.common.NodeContext")
     def test_new_write_permissions(self, context, permissions):
         """User needs write permissions."""
@@ -248,14 +249,17 @@ class NodeCLITest(unittest.TestCase):
 
         self.assertEqual(result.exit_code, 0)
 
+    def _setup_stop_test(self, containers):
+        container1 = MagicMock()
+        container1.name = f"{APPNAME}-iknl-user"
+        containers.list.return_value = [container1]
+
     @patch("docker.DockerClient.containers")
     @patch("vantage6.cli.node.stop.check_docker_running", return_value=True)
     @patch("vantage6.cli.node.stop.NodeContext")
     @patch("vantage6.cli.node.stop.delete_volume_if_exists")
     def test_stop(self, delete_volume, node_context, check_docker, containers):
-        container1 = MagicMock()
-        container1.name = f"{APPNAME}-iknl-user"
-        containers.list.return_value = [container1]
+        self._setup_stop_test(containers)
 
         runner = CliRunner()
 
@@ -267,6 +271,24 @@ class NodeCLITest(unittest.TestCase):
 
         self.assertEqual(result.exit_code, 0)
 
+    @patch("docker.DockerClient.containers")
+    @patch("vantage6.cli.node.stop.check_docker_running", return_value=True)
+    @patch("vantage6.cli.node.stop.NodeContext")
+    @patch("vantage6.cli.node.stop.delete_volume_if_exists")
+    @patch("vantage6.cli.node.restart.subprocess.run")
+    def test_restart(
+        self, subprocess_run, delete_volume, node_context, check_docker, containers
+    ):
+        """Restart a node without errors."""
+        self._setup_stop_test(containers)
+        # The subprocess.run() function is called with the command to start the node.
+        # Unfortunately it is hard to test this, so we just return a successful run
+        subprocess_run.return_value = MagicMock(returncode=0)
+        runner = CliRunner()
+        with runner.isolated_filesystem():
+            result = runner.invoke(cli_node_restart, ["--name", "iknl"])
+        self.assertEqual(result.exit_code, 0)
+
     @patch("vantage6.cli.node.attach.time")
     @patch("vantage6.cli.node.attach.print_log_worker")
     @patch("docker.DockerClient.containers")

tests_cli/test_server_cli.py

@@ -112,7 +112,7 @@ class ServerCLITest(unittest.TestCase):
         self.assertEqual(result.exit_code, 0)
 
     @patch("vantage6.cli.server.new.configuration_wizard")
-    @patch("vantage6.cli.server.new.check_config_writeable")
+    @patch("vantage6.cli.server.new.ensure_config_dir_writable")
     @patch("vantage6.cli.server.new.ServerContext")
     def test_new(self, context, permissions, wizard):
         """New configuration without errors."""

vantage6/cli/_version.py

@@ -7,7 +7,7 @@ with open(os.path.join(here, "__build__")) as fp:
     __build__ = json.load(fp)
 
 # Module version
-version_info = (4, 8, 2, "final", __build__, 0)
+version_info = (4, 9, 0, "final", __build__, 0)
 
 # Module version stage suffix map
 _specifier_ = {"alpha": "a", "beta": "b", "candidate": "rc", "final": ""}

vantage6/cli/algostore/attach.py

@@ -1,19 +1,23 @@
 import click
 import docker
+import questionary as q
 
 from colorama import Fore, Style
 
 from vantage6.common import error
 from vantage6.common.docker.addons import check_docker_running
 from vantage6.common.globals import APPNAME, InstanceType
-from vantage6.cli.common.decorator import click_insert_context
 from vantage6.cli.common.start import attach_logs
-from vantage6.cli.context.algorithm_store import AlgorithmStoreContext
+from vantage6.cli.globals import DEFAULT_SERVER_SYSTEM_FOLDERS
 
 
 @click.command()
-@click_insert_context(InstanceType.ALGORITHM_STORE)
-def cli_algo_store_attach(ctx: AlgorithmStoreContext) -> None:
+@click.option("-n", "--name", default=None, help="configuration name")
+@click.option("--system", "system_folders", flag_value=True)
+@click.option(
+    "--user", "system_folders", flag_value=False, default=DEFAULT_SERVER_SYSTEM_FOLDERS
+)
+def cli_algo_store_attach(name: str, system_folders: bool) -> None:
     """
     Show the server logs in the current console.
     """
@@ -25,8 +29,17 @@ def cli_algo_store_attach(ctx: AlgorithmStoreContext) -> None:
     )
     running_server_names = [container.name for container in running_servers]
 
-    if ctx.docker_container_name in running_server_names:
-        container = client.containers.get(ctx.docker_container_name)
+    if not name:
+        name = q.select(
+            "Select the algorithm store you wish to attach:",
+            choices=running_server_names,
+        ).ask()
+    else:
+        post_fix = "system" if system_folders else "user"
+        name = f"{APPNAME}-{name}-{post_fix}-{InstanceType.ALGORITHM_STORE}"
+
+    if name in running_server_names:
+        container = client.containers.get(name)
         attach_logs(container, InstanceType.ALGORITHM_STORE)
     else:
-        error(f"{Fore.RED}{ctx.name}{Style.RESET_ALL} is not running!")
+        error(f"{Fore.RED}{name}{Style.RESET_ALL} is not running!")

vantage6/cli/algostore/new.py

@@ -1,7 +1,7 @@
 import click
 from colorama import Fore, Style
 
-from vantage6.common import info, error, check_config_writeable
+from vantage6.common import info, error, ensure_config_dir_writable
 from vantage6.common.globals import InstanceType
 from vantage6.cli.globals import DEFAULT_SERVER_SYSTEM_FOLDERS
 from vantage6.cli.context.algorithm_store import AlgorithmStoreContext
@@ -36,7 +36,7 @@ def cli_algo_store_new(name: str, system_folders: bool) -> None:
         exit(1)
 
     # Check that we can write in this folder
-    if not check_config_writeable(system_folders):
+    if not ensure_config_dir_writable(system_folders):
         error("Your user does not have write access to all folders. Exiting")
         info(
             f"Create a new server using '{Fore.GREEN}v6 algorithm-store new "

vantage6/cli/cli.py

@@ -17,6 +17,7 @@ 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.remove import cli_node_remove
+from vantage6.cli.node.restart import cli_node_restart
 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
@@ -75,6 +76,7 @@ cli_node.add_command(cli_node_files, name="files")
 cli_node.add_command(cli_node_list, name="list")
 cli_node.add_command(cli_node_new_configuration, name="new")
 cli_node.add_command(cli_node_remove, name="remove")
+cli_node.add_command(cli_node_restart, name="restart")
 cli_node.add_command(cli_node_set_api_key, name="set-api-key")
 cli_node.add_command(cli_node_start, name="start")
 cli_node.add_command(cli_node_stop, name="stop")

vantage6/cli/common/utils.py

@@ -135,3 +135,22 @@ def print_log_worker(logs_stream: Iterable[bytes]) -> None:
                 "the container."
             )
             print(log)
+
+
+def get_name_from_container_name(container_name: str) -> str:
+    """
+    Get the node/server/store name from a container name.
+
+    Parameters
+    ----------
+    container_name : str
+        The name of the container
+
+    Returns
+    -------
+    str
+        The name of the node/server/store
+    """
+    # Container name is structured as: f"{APPNAME}-{name}-{post_fix}"
+    # Take into account that name can contain '-'
+    return "-".join(container_name.split("-")[1:-1])

vantage6/cli/configuration_wizard.py

@@ -487,7 +487,9 @@ def algo_store_configuration_questionaire(instance_name: str) -> dict:
     """
     config = _get_common_server_config(InstanceType.ALGORITHM_STORE, instance_name)
 
-    default_v6_server_uri = f"http://localhost:{Ports.DEV_SERVER.value}/api"
+    default_v6_server_uri = (
+        f"http://localhost:{Ports.DEV_SERVER.value}{DEFAULT_API_PATH}"
+    )
     default_root_username = "root"
 
     v6_server_uri = q.text(

vantage6/cli/dev/create.py

@@ -485,8 +485,9 @@ def demo_network(
     "--server-url",
     type=str,
     default="http://host.docker.internal",
-    help="Server URL to point to. If you are using Docker Desktop, "
-    "the default http://host.docker.internal should not be changed.",
+    help="Server URL to point to. If you are using Docker Desktop, the default "
+    "http://host.docker.internal should not be changed. If you are using Linux without"
+    " Docker Desktop, you should set this to http://172.17.0.1",
 )
 @click.option(
     "-p",

vantage6/cli/dev/start.py

@@ -67,7 +67,7 @@ def start_demo_network(
     cmd = ["v6", "algorithm-store", "start", "--name", f"{ctx.name}_store", "--user"]
     if store_image:
         cmd.extend(["--image", store_image])
-    subprocess.run(cmd)
+    subprocess.run(cmd, check=True)
 
     # run all nodes that belong to this server
     configs, _ = NodeContext.available_configurations(system_folders=False)
@@ -78,7 +78,7 @@ def start_demo_network(
         cmd = ["v6", "node", "start", "--name", name]
         if node_image:
             cmd.extend(["--image", node_image])
-        subprocess.run(cmd)
+        subprocess.run(cmd, check=True)
 
     # now that both server and store have been started, couple them
     info("Linking local algorithm store to server...")

vantage6/cli/node/attach.py

@@ -46,7 +46,7 @@ def cli_node_attach(name: str, system_folders: bool) -> None:
 
     if not name:
         name = q.select(
-            "Select the node you wish to inspect:", choices=running_node_names
+            "Select the node you wish to attach:", choices=running_node_names
         ).ask()
     else:
         post_fix = "system" if system_folders else "user"

vantage6/cli/node/common/__init__.py

@@ -38,7 +38,9 @@ def create_client(ctx: NodeContext) -> UserClient:
     return UserClient(host, port, api_path, log_level="warn")
 
 
-def create_client_and_authenticate(ctx: NodeContext) -> UserClient:
+def create_client_and_authenticate(
+    ctx: NodeContext, ask_mfa: bool = False
+) -> UserClient:
     """
     Generate a client and authenticate with the server.
 
@@ -46,6 +48,8 @@ def create_client_and_authenticate(ctx: NodeContext) -> UserClient:
     ----------
     ctx : NodeContext
         Context of the node loaded from the configuration file
+    ask_mfa : bool, optional
+        Whether to ask for MFA code, by default False
 
     Returns
     -------
@@ -56,9 +60,10 @@ def create_client_and_authenticate(ctx: NodeContext) -> UserClient:
 
     username = q.text("Username:").ask()
     password = q.password("Password:").ask()
+    mfa_code = q.text("MFA code:").ask() if ask_mfa else None
 
     try:
-        client.authenticate(username, password)
+        client.authenticate(username, password, mfa_code=mfa_code)
 
     except Exception as exc:
         error("Could not authenticate with server!")

vantage6/cli/node/create_private_key.py

@@ -59,6 +59,13 @@ from vantage6.cli.node.common import select_node, create_client_and_authenticate
     default=False,
     help="Overwrite existing private key if present",
 )
+@click.option(
+    "--mfa",
+    "ask_mfa",
+    flag_value=True,
+    default=False,
+    help="Ask for multi-factor authentication code. Use this if MFA is enabled on the server.",
+)
 def cli_node_create_private_key(
     name: str,
     config: str,
@@ -66,6 +73,7 @@ def cli_node_create_private_key(
     upload: bool,
     organization_name: str,
     overwrite: bool,
+    ask_mfa: bool,
 ) -> None:
     """
     Create and upload a new private key
@@ -89,7 +97,7 @@ def cli_node_create_private_key(
     # Authenticate with the server to obtain organization name if it wasn't
     # provided
     if organization_name is None:
-        client = create_client_and_authenticate(ctx)
+        client = create_client_and_authenticate(ctx, ask_mfa)
         organization_name = client.whoami.organization_name
 
     # create directory where private key goes if it doesn't exist yet
@@ -103,7 +111,7 @@ def cli_node_create_private_key(
         warning(f"File '{Fore.CYAN}{file_}{Style.RESET_ALL}' exists!")
 
         if overwrite:
-            warning("'--override' specified, so it will be overwritten ...")
+            warning("'--overwrite' specified, so it will be overwritten ...")
 
     if file_.exists() and not overwrite:
         error("Could not create private key!")

vantage6/cli/node/new.py

@@ -1,7 +1,7 @@
 import click
 from colorama import Fore, Style
 
-from vantage6.common import error, info, check_config_writeable
+from vantage6.common import error, info, ensure_config_dir_writable
 from vantage6.cli.context.node import NodeContext
 from vantage6.cli.globals import DEFAULT_NODE_SYSTEM_FOLDERS as N_FOL
 from vantage6.cli.configuration_wizard import configuration_wizard
@@ -41,7 +41,7 @@ def cli_node_new_configuration(name: str, system_folders: bool) -> None:
         exit(1)
 
     # Check that we can write in this folder
-    if not check_config_writeable(system_folders):
+    if not ensure_config_dir_writable(system_folders):
         error("Cannot write configuration file. Exiting...")
         exit(1)
 

vantage6/cli/node/restart.py

@@ -0,0 +1,124 @@
+import subprocess
+import click
+import questionary as q
+import docker
+
+from vantage6.common import warning, error
+from vantage6.common.docker.addons import check_docker_running
+from vantage6.cli.common.utils import get_name_from_container_name
+from vantage6.cli.node.stop import cli_node_stop
+from vantage6.cli.node.common import find_running_node_names
+from vantage6.cli.globals import DEFAULT_NODE_SYSTEM_FOLDERS as N_FOL
+
+
+@click.command()
+@click.option("-n", "--name", default=None, help="Configuration name")
+@click.option(
+    "--system",
+    "system_folders",
+    flag_value=True,
+    help="Search for configuration in system folders instead of " "user folders",
+)
+@click.option(
+    "--user",
+    "system_folders",
+    flag_value=False,
+    default=N_FOL,
+    help="Search for configuration in the user folders instead of "
+    "system folders. This is the default.",
+)
+@click.option("-i", "--image", default=None, help="Node Docker image to use")
+@click.option(
+    "--keep/--auto-remove",
+    default=False,
+    help="Keep node container after finishing. Useful for debugging",
+)
+@click.option(
+    "--force-db-mount",
+    is_flag=True,
+    help="Always mount node databases; skip the check if they are existing files.",
+)
+@click.option(
+    "--attach/--detach",
+    default=False,
+    help="Show node logs on the current console after starting the " "node",
+)
+@click.option(
+    "--mount-src",
+    default="",
+    help="Override vantage6 source code in container with the source"
+    " code in this path",
+)
+@click.option("--all", "all_nodes", flag_value=True, help="Stop all running nodes")
+@click.option(
+    "--force",
+    "force",
+    flag_value=True,
+    help="Kill nodes instantly; don't wait for them to shut down",
+)
+@click.pass_context
+def cli_node_restart(
+    click_ctx: click.Context,
+    name: str,
+    system_folders: bool,
+    image: str,
+    keep: bool,
+    mount_src: str,
+    attach: bool,
+    force_db_mount: bool,
+    all_nodes: bool,
+    force: bool,
+) -> None:
+    """Restart the node"""
+    check_docker_running()
+    client = docker.from_env()
+
+    running_node_names = find_running_node_names(client)
+    if not running_node_names:
+        warning("No nodes are currently running. No action taken.")
+        return
+
+    if attach and all_nodes:
+        error(
+            "Cannot attach logs of all nodes at once. Please remove either the "
+            "'--all' or '--attach' option."
+        )
+        return
+
+    if all_nodes:
+        names = [
+            get_name_from_container_name(container_name)
+            for container_name in running_node_names
+        ]
+    else:
+        if not name:
+            container_name = q.select(
+                "Select the node you wish to restart:", choices=running_node_names
+            ).ask()
+            names = [get_name_from_container_name(container_name)]
+        else:
+            names = [name]
+
+    for node_name in names:
+        click_ctx.invoke(
+            cli_node_stop,
+            name=node_name,
+            system_folders=system_folders,
+            all_nodes=False,
+            force=force,
+        )
+
+        cmd = ["v6", "node", "start", "--name", node_name]
+        if system_folders:
+            cmd.append("--system")
+        if image:
+            cmd.extend(["--image", image])
+        if keep:
+            cmd.append("--keep")
+        if mount_src:
+            cmd.extend(["--mount-src", mount_src])
+        if attach:
+            cmd.append("--attach")
+        if force_db_mount:
+            cmd.append("--force-db-mount")
+        subprocess.run(cmd, check=True)

vantage6/cli/node/set_api_key.py

@@ -1,7 +1,7 @@
 import click
 import questionary as q
 
-from vantage6.common import error, info, check_config_writeable
+from vantage6.common import error, info, ensure_config_dir_writable
 from vantage6.cli.context.node import NodeContext
 from vantage6.cli.globals import DEFAULT_NODE_SYSTEM_FOLDERS as N_FOL
 from vantage6.cli.configuration_wizard import NodeConfigurationManager
@@ -33,7 +33,7 @@ def cli_node_set_api_key(name: str, api_key: str, system_folders: bool) -> None:
     name = select_node(name, system_folders)
 
     # Check that we can write in the config folder
-    if not check_config_writeable(system_folders):
+    if not ensure_config_dir_writable(system_folders):
         error("Your user does not have write access to all folders. Exiting")
         exit(1)
 

vantage6/cli/node/start.py

@@ -177,7 +177,7 @@ def cli_node_start(
         if Path(fullpath).exists():
             mounts.append(("/mnt/private_key.pem", str(fullpath)))
         else:
-            warning(f"private key file provided {fullpath}, " "but does not exists")
+            warning(f"Private key file is provided {fullpath}, but does not exist")
 
     # Mount private keys for ssh tunnels
     ssh_tunnels = ctx.config.get("ssh-tunnels", [])

vantage6/cli/server/attach.py

@@ -35,7 +35,7 @@ def cli_server_attach(name: str, system_folders: bool) -> None:
 
     if not name:
         name = q.select(
-            "Select the server you wish to inspect:", choices=running_server_names
+            "Select the server you wish to attach:", choices=running_server_names
         ).ask()
     else:
         post_fix = "system" if system_folders else "user"

vantage6/cli/server/new.py

@@ -1,7 +1,7 @@
 import click
 from colorama import Fore, Style
 
-from vantage6.common import info, error, check_config_writeable
+from vantage6.common import info, error, ensure_config_dir_writable
 from vantage6.cli.globals import DEFAULT_SERVER_SYSTEM_FOLDERS
 from vantage6.cli.context.server import ServerContext
 from vantage6.cli.configuration_wizard import configuration_wizard
@@ -36,7 +36,7 @@ def cli_server_new(name: str, system_folders: bool) -> None:
         exit(1)
 
     # Check that we can write in this folder
-    if not check_config_writeable(system_folders):
+    if not ensure_config_dir_writable(system_folders):
         error("Your user does not have write access to all folders. Exiting")
         info(
             f"Create a new server using '{Fore.GREEN}v6 server new "

{vantage6-4.8.2.dist-info → vantage6-4.9.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vantage6
-Version: 4.8.2
+Version: 4.9.0
 Summary: vantage6 command line interface
 Home-page: https://github.com/vantage6/vantage6
 Requires-Python: >=3.10
@@ -16,8 +16,8 @@ Requires-Dist: questionary==1.10.0
 Requires-Dist: rich==13.5.2
 Requires-Dist: schema==0.7.5
 Requires-Dist: SQLAlchemy==1.4.46
-Requires-Dist: vantage6-common==4.8.2
-Requires-Dist: vantage6-client==4.8.2
+Requires-Dist: vantage6-common==4.9.0
+Requires-Dist: vantage6-client==4.9.0
 Provides-Extra: dev
 Requires-Dist: coverage==6.4.4; extra == "dev"
 Requires-Dist: black; extra == "dev"

{vantage6-4.8.2.dist-info → vantage6-4.9.0.dist-info}/RECORD

@@ -1,60 +1,61 @@
 tests_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests_cli/test_example.py,sha256=0fw_v-lgZEacshWSDwLNyLMA1_xc48bKUGM3ll-n1L0,146
-tests_cli/test_node_cli.py,sha256=09qQGsn7vhmIJz9B1sABPuiEfcL2-d8FxhsMUtmXAO0,16066
-tests_cli/test_server_cli.py,sha256=61et2WpcVAr4SAsQTLJEeBy1RnewujMvFgFW6N_i7kg,5863
+tests_cli/test_node_cli.py,sha256=lPRKFK5JsZS-rFV943B9S6BUcHLGLpE9cu53ZBkyjus,17127
+tests_cli/test_server_cli.py,sha256=M0Vh4XZIxZPwPPFDY03pBP3yk98vmmW_2G91BcM0_Yg,5867
 tests_cli/test_wizard.py,sha256=eoa0WQ9yw7IjtaeAKzbK8-sOCBGow7gLrhhmUx024p8,4881
 vantage6/cli/__build__,sha256=X-zrZv_IbzjZUnhsbWlsecLbwjndTpG0ZynXOif7V-k,1
 vantage6/cli/__init__.py,sha256=-Ec-Z7ELDveGdSALXda3qdUGpkuKyJQfhN3eIm7koHE,127
-vantage6/cli/_version.py,sha256=Xt41LiFIQVx6zfbxztkxSnrw5rd9RAlFMcYxqQC8CS4,696
-vantage6/cli/cli.py,sha256=AecGqgdDI_IaAbedeRN9F8E3hvSpqfbG9Ot7LiAfBTs,6074
+vantage6/cli/_version.py,sha256=5_N7ID4mlQDdbdXKu-RHvKbEzw5nS7_2FSKr8IbNw0I,696
+vantage6/cli/cli.py,sha256=NHpiPcljADaVzwGYrG4FWVMfbmDRguSZWBeGxcdQxDo,6184
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@@ -68,8 +69,8 @@ vantage6/cli/template/server_import_config.j2,sha256=9WT2XeG9-ADoYLb4ahXhof3i9Fc
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