vantage6 5.0.0a36__py3-none-any.whl → 5.0.0a38__py3-none-any.whl

vantage6/cli/context/server.py

@@ -36,12 +36,14 @@ class ServerContext(BaseServerContext):
         instance_name: str,
         system_folders: bool = S_FOL,
         in_container: bool = False,
+        is_sandbox: bool = False,
     ):
         super().__init__(
             InstanceType.SERVER,
             instance_name,
             system_folders=system_folders,
             in_container=in_container,
+            is_sandbox=is_sandbox,
         )
         self.log.info("vantage6 version '%s'", __version__)
 
@@ -123,7 +125,9 @@ class ServerContext(BaseServerContext):
         )
 
     @classmethod
-    def config_exists(cls, instance_name: str, system_folders: bool = S_FOL) -> bool:
+    def config_exists(
+        cls, instance_name: str, system_folders: bool = S_FOL, is_sandbox: bool = False
+    ) -> bool:
         """
         Check if a configuration file exists.
 
@@ -134,19 +138,23 @@ class ServerContext(BaseServerContext):
             of the configuration file.
         system_folders : bool, optional
             System wide or user configuration, by default S_FOL
-
+        is_sandbox : bool, optional
+            Whether the configuration is a sandbox configuration, by default False
         Returns
         -------
         bool
             Whether the configuration file exists or not
         """
-        return super().config_exists(
-            InstanceType.SERVER, instance_name, system_folders=system_folders
+        return super().base_config_exists(
+            InstanceType.SERVER,
+            instance_name,
+            system_folders=system_folders,
+            is_sandbox=is_sandbox,
         )
 
     @classmethod
     def available_configurations(
-        cls, system_folders: bool = S_FOL
+        cls, system_folders: bool = S_FOL, is_sandbox: bool = False
     ) -> tuple[list, list]:
         """
         Find all available server configurations in the default folders.
@@ -155,6 +163,8 @@ class ServerContext(BaseServerContext):
         ----------
         system_folders : bool, optional
             System wide or user configuration, by default S_FOL
+        is_sandbox : bool, optional
+            Whether the configuration is a sandbox configuration, by default False
 
         Returns
         -------
@@ -162,4 +172,6 @@ class ServerContext(BaseServerContext):
             The first list contains validated configuration files, the second
             list contains invalid configuration files.
         """
-        return super().available_configurations(InstanceType.SERVER, system_folders)
+        return super().available_configurations(
+            InstanceType.SERVER, system_folders, is_sandbox
+        )

vantage6/cli/globals.py

@@ -96,6 +96,7 @@ class CLICommandName(StrEnumBase):
     NODE = "node"
     ALGORITHM = "algorithm"
     TEST = "test"
+    SANDBOX = "sandbox"
     DEV = "dev"
     USE = "use"
     AUTH = "auth"

vantage6/cli/node/attach.py

@@ -2,13 +2,37 @@ import click
 
 from vantage6.common import info
 
-from vantage6.cli.common.utils import attach_logs
+from vantage6.cli.common.attach import attach_logs
+from vantage6.cli.context import InstanceType
+from vantage6.cli.globals import InfraComponentName
 
 
 @click.command()
-def cli_node_attach() -> None:
+@click.option("-n", "--name", default=None, help="Name of the configuration")
+@click.option("--system", "system_folders", flag_value=True, help="Use system folders")
+@click.option("--user", "system_folders", flag_value=False, help="Use user folders")
+@click.option("--context", default=None, help="Kubernetes context to use")
+@click.option("--namespace", default=None, help="Kubernetes namespace to use")
+@click.option(
+    "--sandbox", "is_sandbox", flag_value=True, help="Attach to a sandbox environment"
+)
+def cli_node_attach(
+    name: str | None,
+    system_folders: bool,
+    context: str,
+    namespace: str,
+    is_sandbox: bool,
+) -> None:
     """
     Show the node logs in the current console.
     """
     info("Attaching to node logs...")
-    attach_logs("app=node")
+    attach_logs(
+        name,
+        instance_type=InstanceType.NODE,
+        infra_component=InfraComponentName.NODE,
+        system_folders=system_folders,
+        context=context,
+        namespace=namespace,
+        is_sandbox=is_sandbox,
+    )

vantage6/cli/node/common/__init__.py

@@ -8,11 +8,16 @@ import docker
 from colorama import Fore, Style
 
 from vantage6.common import debug, error, info
-from vantage6.common.globals import APPNAME, InstanceType, RequiredNodeEnvVars
+from vantage6.common.globals import (
+    APPNAME,
+    HTTP_LOCALHOST,
+    InstanceType,
+    RequiredNodeEnvVars,
+)
 
 from vantage6.client import UserClient
 
-from vantage6.cli.configuration_wizard import select_configuration_questionaire
+from vantage6.cli.configuration_create import select_configuration_questionnaire
 from vantage6.cli.context.node import NodeContext
 
 
@@ -33,7 +38,7 @@ def create_client(ctx: NodeContext) -> UserClient:
     # 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"
+        host = HTTP_LOCALHOST
     port = ctx.config["port"]
     api_path = ctx.config["api_path"]
     info(f"Connecting to server at '{host}:{port}{api_path}'")
@@ -64,26 +69,37 @@ def create_client_and_authenticate(ctx: NodeContext) -> UserClient:
         client.authenticate()
     except Exception as exc:
         error("Could not authenticate with server!")
-        debug(exc)
+        debug(str(exc))
         exit(1)
 
     return client
 
 
-def select_node(name: str, system_folders: bool) -> tuple[str, str]:
+def select_node(name: str, system_folders: bool) -> str:
     """
     Let user select node through questionnaire if name is not given.
 
+    Parameters
+    ----------
+    name : str
+        Name of the node to select
+    system_folders : bool
+        Whether to use system folders or not
+
     Returns
     -------
     str
         Name of the configuration file
     """
-    name = (
-        name
-        if name
-        else select_configuration_questionaire(InstanceType.NODE, system_folders)
-    )
+    try:
+        name = (
+            name
+            if name
+            else select_configuration_questionnaire(InstanceType.NODE, system_folders)
+        )
+    except Exception:
+        error("No configurations could be found!")
+        exit()
 
     # raise error if config could not be found
     if not NodeContext.config_exists(name, system_folders):

vantage6/cli/node/common/task_cleanup.py

@@ -0,0 +1,153 @@
+import logging
+
+from kubernetes import client as k8s_client
+from kubernetes.client.rest import ApiException
+
+from vantage6.common import logger_name
+
+log = logging.getLogger(logger_name(__name__))
+
+
+def delete_job_related_pods(
+    run_id: int,
+    container_name: str,
+    namespace: str,
+    core_api: k8s_client.CoreV1Api,
+    batch_api: k8s_client.BatchV1Api,
+) -> None:
+    """
+    Deletes all the PODs created by a Kubernetes job in a given namespace
+
+    Parameters
+    ----------
+    run_id: int
+        Server run identifier
+    container_name: str
+        Name of the container
+    namespace: str
+        Namespace where the container is located
+    core_api: k8s_client.CoreV1Api
+        Kubernetes Core API instance
+    batch_api: k8s_client.BatchV1Api
+        Kubernetes Batch API instance
+    """
+    log.info(
+        "Cleaning up kubernetes Job %s (run_id = %s) and related PODs",
+        container_name,
+        run_id,
+    )
+
+    __delete_job(container_name, namespace, batch_api)
+
+    job_selector = f"job-name={container_name}"
+    job_pods_list = core_api.list_namespaced_pod(namespace, label_selector=job_selector)
+    for job_pod in job_pods_list.items:
+        __delete_pod(job_pod.metadata.name, namespace, core_api)
+
+    __delete_secret(container_name, namespace, core_api)
+
+
+def __delete_secret(
+    secret_name: str, namespace: str, core_api: k8s_client.CoreV1Api
+) -> None:
+    """
+    Deletes a secret in a given namespace
+
+    Parameters
+    ----------
+    secret_name: str
+        Name of the secret
+    namespace: str
+        Namespace where the secret is located
+    core_api: k8s_client.CoreV1Api
+        Kubernetes Core API instance
+    """
+    try:
+        core_api.delete_namespaced_secret(name=secret_name, namespace=namespace)
+        log.info(
+            "Removed kubernetes Secret %s in namespace %s",
+            secret_name,
+            namespace,
+        )
+    except ApiException as exc:
+        if exc.status == 404:
+            log.debug("No secret %s to remove in namespace %s", secret_name, namespace)
+        else:
+            log.error("Exception when deleting namespaced secret: %s", exc)
+
+
+def __delete_job(
+    job_name: str, namespace: str, batch_api: k8s_client.BatchV1Api
+) -> None:
+    """
+    Deletes a job in a given namespace
+
+    Parameters
+    ----------
+    job_name: str
+        Name of the job
+    namespace: str
+        Namespace where the job is located
+    batch_api: k8s_client.BatchV1Api
+        Kubernetes Batch API instance
+    """
+    log.info(
+        "Cleaning up kubernetes Job %s and related PODs",
+        job_name,
+    )
+    try:
+        # Check if the job exists before attempting to delete it
+        job = batch_api.read_namespaced_job(name=job_name, namespace=namespace)
+        if job:
+            batch_api.delete_namespaced_job(name=job_name, namespace=namespace)
+        else:
+            log.warning(
+                "Job %s not found in namespace %s, skipping deletion",
+                job_name,
+                namespace,
+            )
+    except ApiException as exc:
+        if exc.status == 404:
+            log.warning(
+                "Job %s not found in namespace %s, skipping deletion",
+                job_name,
+                namespace,
+            )
+        else:
+            log.error("Exception when deleting namespaced job: %s", exc)
+
+
+def __delete_pod(pod_name: str, namespace: str, core_api: k8s_client.CoreV1Api) -> None:
+    """
+    Deletes a job in a given namespace
+
+    Parameters
+    ----------
+    pod_name: str
+        Name of the job
+    namespace: str
+        Namespace where the job is located
+    core_api: k8s_client.CoreV1Api
+        Kubernetes Core API instance
+    """
+    log.info("Cleaning up kubernetes pod %s in namespace %s", pod_name, namespace)
+    try:
+        # Check if the job exists before attempting to delete it
+        job = core_api.read_namespaced_pod(name=pod_name, namespace=namespace)
+        if job:
+            core_api.delete_namespaced_pod(name=pod_name, namespace=namespace)
+        else:
+            log.warning(
+                "Pod %s not found in namespace %s, skipping deletion",
+                pod_name,
+                namespace,
+            )
+    except ApiException as exc:
+        if exc.status == 404:
+            log.warning(
+                "Pod %s not found in namespace %s, skipping deletion",
+                pod_name,
+                namespace,
+            )
+        else:
+            log.error("Exception when deleting namespaced job: %s", exc)

vantage6/cli/node/list.py

@@ -1,13 +1,8 @@
 import click
-import docker
-from colorama import Fore, Style
 
-from vantage6.common import warning
-from vantage6.common.docker.addons import check_docker_running
-from vantage6.common.globals import APPNAME
+from vantage6.common.globals import InstanceType
 
-from vantage6.cli.context.node import NodeContext
-from vantage6.cli.node.common import find_running_node_names
+from vantage6.cli.common.list import get_configuration_list
 
 
 @click.command()
@@ -18,40 +13,4 @@ def cli_node_list() -> None:
     Note that this command cannot find node configuration files in custom
     directories.
     """
-
-    check_docker_running()
-    client = docker.from_env()
-
-    running_node_names = find_running_node_names(client)
-
-    header = "\nName" + (21 * " ") + "Status" + (10 * " ") + "System/User"
-
-    click.echo(header)
-    click.echo("-" * len(header))
-
-    running = Fore.GREEN + "Running" + Style.RESET_ALL
-    stopped = Fore.RED + "Not running" + Style.RESET_ALL
-
-    # system folders
-    configs, f1 = NodeContext.available_configurations(system_folders=True)
-    for config in configs:
-        status = (
-            running
-            if f"{APPNAME}-{config.name}-system" in running_node_names
-            else stopped
-        )
-        click.echo(f"{config.name:25}{status:25}System ")
-
-    # user folders
-    configs, f2 = NodeContext.available_configurations(system_folders=False)
-    for config in configs:
-        status = (
-            running
-            if f"{APPNAME}-{config.name}-user" in running_node_names
-            else stopped
-        )
-        click.echo(f"{config.name:25}{status:25}User   ")
-
-    click.echo("-" * 53)
-    if len(f1) + len(f2):
-        warning(f"{Fore.RED}Failed imports: {len(f1) + len(f2)}{Style.RESET_ALL}")
+    get_configuration_list(InstanceType.NODE)

vantage6/cli/node/new.py

@@ -6,8 +6,10 @@ import questionary as q
 
 from vantage6.common import error, info, warning
 from vantage6.common.client.node_client import NodeClient
+from vantage6.common.context import AppContext
 from vantage6.common.globals import (
     FILE_BASED_DATABASE_TYPES,
+    HTTP_LOCALHOST,
     SERVICE_BASED_DATABASE_TYPES,
     InstanceType,
     NodePolicy,
@@ -17,6 +19,7 @@ from vantage6.common.globals import (
 
 from vantage6.cli.common.new import new
 from vantage6.cli.globals import DEFAULT_NODE_SYSTEM_FOLDERS as N_FOL
+from vantage6.cli.utils import prompt_config_name
 
 
 @click.command()
@@ -52,8 +55,12 @@ def cli_node_new_configuration(
     Checks if the configuration already exists. If this is not the case
     a questionnaire is invoked to create a new configuration file.
     """
+    name = prompt_config_name(name)
+    dirs = AppContext.instance_folders(InstanceType.NODE, name, system_folders)
+    default_data_dir = str(dirs["data"])
     new(
-        questionnaire_function=node_configuration_questionaire,
+        config_producing_func=node_configuration_questionaire,
+        config_producing_func_args=(default_data_dir, name),
         name=name,
         system_folders=system_folders,
         namespace=namespace,
@@ -62,14 +69,14 @@ def cli_node_new_configuration(
     )
 
 
-def node_configuration_questionaire(dirs: dict, instance_name: str) -> dict:
+def node_configuration_questionaire(data_dir: str, instance_name: str) -> dict:
     """
     Questionary to generate a config file for the node instance.
 
     Parameters
     ----------
-    dirs : dict
-        Dictionary with the directories of the node instance.
+    data_dir : str
+        Path to the data directory of the node instance.
     instance_name : str
         Name of the node instance.
 
@@ -85,7 +92,7 @@ def node_configuration_questionaire(dirs: dict, instance_name: str) -> dict:
                 "type": "text",
                 "name": "server_url",
                 "message": "The base-URL of the server:",
-                "default": "http://localhost",
+                "default": HTTP_LOCALHOST,
             },
         ]
     )
@@ -117,7 +124,7 @@ def node_configuration_questionaire(dirs: dict, instance_name: str) -> dict:
                 "type": "text",
                 "name": "task_dir",
                 "message": "Task directory path:",
-                "default": str(dirs["data"]),
+                "default": data_dir,
             },
         ]
     )

vantage6/cli/node/set_api_key.py

@@ -3,7 +3,7 @@ import questionary as q
 
 from vantage6.common import ensure_config_dir_writable, error, info
 
-from vantage6.cli.configuration_wizard import NodeConfigurationManager
+from vantage6.cli.configuration_create import NodeConfigurationManager
 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

vantage6/cli/node/start.py

@@ -3,6 +3,7 @@ import click
 from vantage6.common import info
 from vantage6.common.globals import InstanceType
 
+from vantage6.cli.common.attach import attach_logs
 from vantage6.cli.common.decorator import click_insert_context
 from vantage6.cli.common.start import (
     helm_install,
@@ -10,11 +11,11 @@ from vantage6.cli.common.start import (
     start_port_forward,
 )
 from vantage6.cli.common.utils import (
-    attach_logs,
     create_directory_if_not_exists,
+    select_context_and_namespace,
 )
 from vantage6.cli.context.node import NodeContext
-from vantage6.cli.globals import ChartName
+from vantage6.cli.globals import ChartName, InfraComponentName
 
 from vantage6.node.globals import DEFAULT_PROXY_SERVER_PORT
 
@@ -27,7 +28,14 @@ from vantage6.node.globals import DEFAULT_PROXY_SERVER_PORT
     default=False,
     help="Show node logs on the current console after starting the node",
 )
-@click_insert_context(InstanceType.NODE, include_name=True, include_system_folders=True)
+@click.option("--local-chart-dir", default=None, help="Local chart directory to use")
+@click.option("--sandbox/--no-sandbox", "sandbox", default=False)
+@click_insert_context(
+    InstanceType.NODE,
+    include_name=True,
+    include_system_folders=True,
+    sandbox_param="sandbox",
+)
 def cli_node_start(
     ctx: NodeContext,
     name: str,
@@ -35,13 +43,19 @@ def cli_node_start(
     context: str,
     namespace: str,
     attach: bool,
+    local_chart_dir: str,
 ) -> None:
     """
     Start the node.
     """
     info("Starting node...")
 
-    prestart_checks(ctx, InstanceType.NODE, name, system_folders, context, namespace)
+    prestart_checks(ctx, InstanceType.NODE, name, system_folders)
+
+    context, namespace = select_context_and_namespace(
+        context=context,
+        namespace=namespace,
+    )
 
     create_directory_if_not_exists(ctx.log_dir)
     create_directory_if_not_exists(ctx.data_dir)
@@ -96,16 +110,25 @@ def cli_node_start(
         values_file=ctx.config_file,
         context=context,
         namespace=namespace,
+        local_chart_dir=local_chart_dir,
     )
 
     # start port forward for the node proxy server
     start_port_forward(
         service_name=f"{ctx.helm_release_name}-node-service",
-        service_port=ctx.config["node"].get("port", DEFAULT_PROXY_SERVER_PORT),
-        port=ctx.config["node"].get("port", DEFAULT_PROXY_SERVER_PORT),
+        service_port=ctx.config["node"].get("proxyPort", DEFAULT_PROXY_SERVER_PORT),
+        port=ctx.config["node"].get("proxyPort", DEFAULT_PROXY_SERVER_PORT),
         context=context,
         namespace=namespace,
     )
 
     if attach:
-        attach_logs("app=node")
+        attach_logs(
+            name,
+            instance_type=InstanceType.NODE,
+            infra_component=InfraComponentName.NODE,
+            system_folders=system_folders,
+            context=context,
+            namespace=namespace,
+            is_sandbox=ctx.is_sandbox,
+        )