vantage6 5.0.0a22__py3-none-any.whl → 5.0.0a29__py3-none-any.whl

vantage6/cli/test/algo_test_scripts/algo_test_arguments.py

@@ -0,0 +1,29 @@
+average = {
+    "collaboration": 1,
+    "organizations": [1],
+    "name": "test_average_task",
+    "image": "harbor2.vantage6.ai/demo/average",
+    "description": "",
+    "method": "central_average",
+    "arguments": {
+        "column_name": "Age",
+    },
+    "databases": [{"label": "olympic_athletes"}],
+}
+
+kaplan_meier = {
+    "collaboration": 1,
+    "organizations": [1],
+    "name": "test_average_task",
+    "image": "harbor2.vantage6.ai/algorithms/kaplan-meier",
+    "description": "",
+    "method": "kaplan_meier_central",
+    "arguments": {
+        "time_column_name": "days",
+        "censor_column_name": "censor",
+        "organizations_to_include": [1, 2, 3],
+    },
+    "databases": [{"label": "kaplan_meier_test"}],
+}
+
+args = {"average": average, "kaplan_meier": kaplan_meier}

vantage6/cli/test/algo_test_scripts/algo_test_script.py

@@ -0,0 +1,92 @@
+import json
+import logging
+import sys
+
+from vantage6.common import error
+from vantage6.common.enum import TaskStatus
+from vantage6.common.globals import Ports
+
+from vantage6.client import Client
+
+import vantage6.cli.test.algo_test_scripts.algo_test_arguments as arguments
+
+
+def create_and_run_task(client: Client, task_args: dict, algo_name: str = "algorithm"):
+    """
+    Create and run a task using the provided client and task arguments.
+
+    Parameters
+    ----------
+        client: Client
+            The client instance to use for creating and running the task.
+        task_args: dict
+            The arguments to pass to the task creation method.
+        algo_name: str, optional
+            The name of the algorithm for logging purposes. Default is "algorithm".
+
+    Raises
+    ------
+        AssertionError: If the task fails.
+    """
+    task = client.task.create(**task_args)
+    task_id = task["id"]
+    client.wait_for_results(task_id)
+
+    try:
+        # check if the task has failed
+        assert client.task.get(task_id)["status"] != TaskStatus.FAILED
+
+        logging.info("Task for %s completed successfully.", algo_name)
+
+    except AssertionError:
+        error(
+            f"Task for {algo_name} failed. Check the log file of the task "
+            f"{task_id} for more information."
+        )
+        exit(1)
+
+
+def run_test(custom_args: dict | None = None):
+    """
+    Run a test by creating and running tasks using the provided arguments.
+
+    Parameters
+    ----------
+    custom_args: dict, optional
+        The arguments to pass to the task creation method. If not provided,
+        the arguments from the `arguments` module will be used.
+    """
+    # Create a client and authenticate
+    client = Client(
+        server_url=f"http://localhost:{Ports.DEV_SERVER}/api",
+        auth_url="http://localhost:8080",
+    )
+    try:
+        client.authenticate()
+    except ConnectionError:
+        error(
+            "Could not connect to the server. Please check if a dev network is running."
+        )
+        exit(1)
+
+    # if custom arguments are provided, use them for running the task
+    if custom_args:
+        create_and_run_task(client, custom_args)
+
+    else:
+        # Run the task for each algorithm in the arguments file
+        for algo, task_args in arguments.args.items():
+            logging.info("Running task for %s", algo)
+            logging.info("Task arguments: %s", task_args)
+            create_and_run_task(client, task_args, algo)
+
+
+if __name__ == "__main__":
+    # check if arguments are provided
+    if len(sys.argv) > 1:
+        input_string = sys.argv[1].replace("'", '"')
+        json_input = json.loads(input_string)
+    else:
+        json_input = None
+
+    run_test(json_input)

vantage6/cli/test/client_script.py

@@ -0,0 +1,151 @@
+# import click
+# import json
+# import subprocess
+# import sys
+
+# from pathlib import Path
+
+# from rich.console import Console
+
+# from vantage6.cli.dev.create import create_demo_network
+# from vantage6.cli.dev.remove import remove_demo_network
+
+# # from vantage6.cli.dev.start import start_demo_network
+# # from vantage6.cli.dev.stop import stop_demo_network
+# from vantage6.cli.utils import prompt_config_name
+# from vantage6.common.globals import Ports
+
+# TEST_FILE_PATH = Path(__file__).parent / "algo_test_scripts" / "algo_test_script.py"
+
+
+# @click.command()
+# @click.option(
+#     "--script",
+#     type=click.Path(),
+#     default=TEST_FILE_PATH,
+#     help="Path of the script to test the algorithm. If a script is not provided, the default script is used.",
+# )
+# @click.option(
+#     "--task-arguments",
+#     type=str,
+#     default=None,
+#     help="Arguments to be provided to Task.create function. If --script is provided, this should not be set.",
+# )
+# @click.option(
+#     "--create-dev-network",
+#     is_flag=True,
+#     help="Create a new dev network to run the test",
+# )
+# @click.option(
+#     "--start-dev-network",
+#     is_flag=True,
+#     help="Start a dev network to run the test",
+# )
+# @click.option(
+#     "-n", "--name", default=None, type=str, help="Name for your development setup"
+# )
+# @click.option(
+#     "--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.",
+# )
+# @click.option(
+#     "-i", "--image", type=str, default=None, help="Server Docker image to use"
+# )
+# @click.option(
+#     "--keep",
+#     type=bool,
+#     default=False,
+#     help="Keep the dev network after finishing the test",
+# )
+# @click.option(
+#     "--add-dataset",
+#     type=(str, click.Path()),
+#     default=[],
+#     multiple=True,
+#     help="Add a dataset to the nodes. The first argument is the label of the database, "
+#     "the second is the path to the dataset file.",
+# )
+# @click.pass_context
+# def cli_test_client_script(
+#     click_ctx: click.Context,
+#     script: Path | None,
+#     task_arguments: str | None,
+#     name: str,
+#     server_url: str,
+#     create_dev_network: bool,
+#     start_dev_network: bool,
+#     image: str,
+#     keep: bool,
+#     add_dataset: list[tuple[str, Path]] = (),
+# ) -> int:
+#     """
+#     Run a script for testing an algorithm on a dev network.
+#     The path to the script must be provided as an argument.
+#     """
+#     if not (script or task_arguments):
+#         raise click.UsageError("--script or --task-arguments must be set.")
+#     elif script != TEST_FILE_PATH and task_arguments:
+#         raise click.UsageError("--script and --task-arguments cannot be set together.")
+
+#     # Check if the task_arguments is a valid JSON string
+#     if task_arguments:
+#         try:
+#             json.loads(task_arguments.replace("'", '"'))
+#         except json.JSONDecodeError:
+#             raise click.UsageError("task-arguments must be a valid JSON string.")
+
+#     name = prompt_config_name(name)
+
+#     # create the network
+#     if create_dev_network:
+#         click_ctx.invoke(
+#             create_demo_network,
+#             name=name,
+#             num_nodes=3,
+#             server_url=server_url,
+#             server_port=Ports.DEV_SERVER.value,
+#             image=image,
+#             extra_server_config=None,
+#             extra_node_config=None,
+#             add_dataset=add_dataset,
+#         )
+
+#     # start the server and nodes
+#     if create_dev_network or start_dev_network:
+#         click_ctx.invoke(
+#             start_demo_network,
+#             name=name,
+#             server_image=image,
+#             node_image=image,
+#         )
+
+#     # run the test script and get the result
+#     if not task_arguments:
+#         subprocess_args = ["python", script]
+#     else:
+#         subprocess_args = ["python", script, task_arguments]
+
+#     result = subprocess.run(subprocess_args, stdout=sys.stdout, stderr=sys.stderr)
+
+#     # check the exit code. If the test passed, it should be 0
+#     if result.returncode == 0:
+#         msg = ":heavy_check_mark: [green]Test passed[/green]"
+#     else:
+#         msg = ":x: [red]Test failed[/red]"
+
+#     console = Console()
+#     console.print(msg)
+
+#     # clean up the test resources. Keep the network if --keep is set, or if the network
+#     # was created for this test. If the network was started for this test, stop it but
+#     # do not remove it.
+#     if not keep:
+#         if create_dev_network or start_dev_network:
+#             click_ctx.invoke(stop_demo_network, name=name)
+#         if create_dev_network:
+#             click_ctx.invoke(remove_demo_network, name=name)
+
+#     return result.returncode

vantage6/cli/test/common/diagnostic_runner.py

@@ -122,8 +122,8 @@ class DiagnosticRunner:
             description="VPN Diagnostic test",
             image=DIAGNOSTICS_IMAGE,
             method="vpn_features",
-            input_={
-                "kwargs": {"other_nodes": self.organization_ids},
+            arguments={
+                "other_nodes": self.organization_ids,
             },
             organizations=self.organization_ids,
         )

vantage6/cli/test/feature_tester.py

@@ -1,17 +1,20 @@
 import sys
+
 import click
 
 from vantage6.common.globals import Ports
+
 from vantage6.client import UserClient
-from vantage6.cli.utils import error
+
 from vantage6.cli.test.common.diagnostic_runner import DiagnosticRunner
+from vantage6.cli.utils import error
 
 
 @click.command()
 @click.option(
     "--server-url",
     type=str,
-    default=f"http://localhost:{Ports.DEV_SERVER.value}/api",
+    default=f"http://localhost:{Ports.DEV_SERVER}/api",
     help="URL of the server",
 )
 @click.option(

vantage6/cli/use/context.py

@@ -0,0 +1,46 @@
+import click
+import questionary
+from kubernetes import config
+
+from vantage6.common import error
+
+from vantage6.cli.config import CliConfig
+from vantage6.cli.utils import switch_context_and_namespace
+
+
+@click.command()
+@click.argument("context", required=False, type=str, default=None)
+def cli_use_context(context: str):
+    """
+    Set which Kubernetes context to use.
+    """
+    # Get available contexts
+    contexts, active_context = config.list_kube_config_contexts()
+    context_names = [ctx["name"] for ctx in contexts]
+
+    # Prompt user to select a context
+    if not context:
+        current = active_context["name"] if active_context else None
+        context = questionary.select(
+            "Which Kubernetes context do you want to use?",
+            choices=context_names,
+            default=current if current in context_names else None,
+        ).ask()
+
+        # If no context is selected (e.g. KeyboardInterrupt), exit
+        if not context:
+            return
+
+    # Load the selected context
+    try:
+        config.load_kube_config(context=context)
+    except Exception:
+        error(f"Cannot not find {context} in kube config")
+        return
+
+    # Update kubeconfig current-context
+    switch_context_and_namespace(context=context)
+
+    # Clear the last_context in CLI config
+    cli_config = CliConfig()
+    cli_config.remove_kube()

vantage6/cli/use/namespace.py

@@ -0,0 +1,55 @@
+import click
+import questionary
+from kubernetes import client, config
+
+from vantage6.cli.config import CliConfig
+from vantage6.cli.utils import switch_context_and_namespace
+from vantage6.common import error
+
+
+@click.command()
+@click.argument("namespace", required=False, type=str, default=None)
+def cli_use_namespace(namespace: str):
+    """
+    Set which Kubernetes namespace to use.
+
+    The namespace will be created if it does not exist.
+    """
+    # Load the active context configuration
+    config.load_kube_config()
+
+    try:
+        v1 = client.CoreV1Api()
+        namespace_list = v1.list_namespace()
+    except Exception:
+        error(
+            "Failed to connect to Kubernetes cluster. Check if the cluster is running and reachable."
+        )
+        return
+
+    namespace_names = [ns.metadata.name for ns in namespace_list.items]
+
+    # Prompt user to select a namespace
+    if not namespace:
+        namespace = questionary.select(
+            "Which Kubernetes namespace do you want to use?",
+            choices=namespace_names,
+        ).ask()
+
+        # If no namespace is selected (e.g. KeyboardInterrupt), exit
+        if not namespace:
+            return
+
+    # Check if namespace exists, create if not
+    if namespace not in namespace_names:
+        namespace_body = client.V1Namespace(
+            metadata=client.V1ObjectMeta(name=namespace)
+        )
+        v1.create_namespace(namespace_body)
+
+    # Switch to the selected namespace for current context
+    switch_context_and_namespace(namespace=namespace)
+
+    # Remove the last_context in CLI config
+    cli_config = CliConfig()
+    cli_config.remove_kube()

vantage6/cli/utils.py

@@ -4,14 +4,15 @@ Utility functions for the CLI
 
 from __future__ import annotations
 
+import os
 import re
+import subprocess
+from pathlib import Path
+
 import docker
-import os
 import questionary as q
 
-from pathlib import Path
-
-from vantage6.common import error, warning, info
+from vantage6.common import error, info, warning
 
 
 def check_config_name_allowed(name: str) -> None:
@@ -99,3 +100,68 @@ def prompt_config_name(name: str | None) -> None:
             name = name.replace(" ", "-")
             info(f"Replaced spaces from configuration name: {name}")
     return name
+
+
+def switch_context_and_namespace(
+    context: str | None = None, namespace: str | None = None
+) -> None:
+    # input validation
+    validate_input_cmd_args(context, "context name", allow_none=True)
+    validate_input_cmd_args(namespace, "namespace name", allow_none=True)
+
+    try:
+        if context:
+            subprocess.run(
+                ["kubectl", "config", "use-context", context],
+                check=True,
+                stdout=subprocess.DEVNULL,
+            )
+            info(f"Successfully set context to: {context}")
+
+        if namespace:
+            subprocess.run(
+                [
+                    "kubectl",
+                    "config",
+                    "set-context",
+                    context or "--current",
+                    f"--namespace={namespace}",
+                ],
+                check=True,
+                stdout=subprocess.DEVNULL,
+            )
+            info(f"Successfully set namespace to: {namespace}")
+
+    except subprocess.CalledProcessError as e:
+        error(f"Failed to set Kubernetes context or namespace: {e}")
+
+
+def validate_input_cmd_args(
+    value: str | None, field_name: str, allow_none: bool = False
+) -> None:
+    """
+    Validate input for subprocess commands.
+
+    Parameters
+    ----------
+    value : str | None
+        The value to validate.
+    field_name : str
+        The name of the field being validated, used for error messages.
+    allow_none : bool, optional
+        Whether None is allowed as a valid value. Defaults to False.
+
+    Raises
+    ------
+    SystemExit
+        If the input is invalid.
+    """
+    if allow_none and value is None:
+        return
+
+    if not isinstance(value, str) or not re.match("^[a-zA-Z0-9_.-]+$", value):
+        error(
+            f"Invalid {field_name}: {value}. Use only alphanumeric characters, "
+            "dashes, underscores, or dots."
+        )
+        exit(1)

{vantage6-5.0.0a22.dist-info → vantage6-5.0.0a29.dist-info}/METADATA

@@ -1,9 +1,9 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: vantage6
-Version: 5.0.0a22
+Version: 5.0.0a29
 Summary: vantage6 command line interface
 Home-page: https://github.com/vantage6/vantage6
-Requires-Python: >=3.10
+Requires-Python: >=3.13
 Description-Content-Type: text/markdown
 Requires-Dist: click==8.1.3
 Requires-Dist: colorama==0.4.6
@@ -11,17 +11,25 @@ Requires-Dist: copier==9.2.0
 Requires-Dist: docker==7.1.0
 Requires-Dist: ipython==8.10.0
 Requires-Dist: jinja2==3.1.6
-Requires-Dist: pandas>=1.5.3
+Requires-Dist: kubernetes==28.1.0
+Requires-Dist: pandas>=2.2.3
 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-common==5.0.0a22
-Requires-Dist: vantage6-client==5.0.0a22
+Requires-Dist: vantage6-common==5.0.0a29
+Requires-Dist: vantage6-client==5.0.0a29
 Provides-Extra: dev
 Requires-Dist: coverage==6.4.4; extra == "dev"
 Requires-Dist: black; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 <h1 align="center">
   <br>
@@ -70,7 +78,7 @@ collaborations. The server contains users, organizations, collaborations, tasks
 their results. It provides a central access point for both the clients and nodes. The
 nodes have access to privacy sensitive data and handle computation requests retrieved
 from the server. Computation request are executed as separate containers on the node.
-These containers are connected to containers at other nodes by a VPN network._
+These containers are connected to containers at other nodes by a internal network._
 
 ## :books: Quickstart
 
@@ -185,11 +193,7 @@ with `VERSION` being the full semantic version of the vantage6 infrastructure, e
 Several other images are used to support the infrastructure:
 
 - `harbor2.vantage6.ai/infrastructure/infrastructure-base:VERSION` -> _Base image for the infrastructure_
-- `harbor2.vantage6.ai/infrastructure/squid:VERSION` -> _Squid proxy image used for the whitelisting service_
 - `harbor2.vantage6.ai/infrastructure/alpine` -> _Alpine image used for vpn traffic forwarding_
-- `harbor2.vantage6.ai/infrastructure/vpn-client` -> _VPN image used to connect to the VPN_
-- `harbor2.vantage6.ai/infrastructure/vpn-configurator` -> _VPN image used for initialization_
-- `harbor2.vantage6.ai/infrastructure/ssh-tunnel` -> _SSH tunnel image used for connecting algorithms to external services_
 
 And finally there are some images released for algorithm development:
 

vantage6-5.0.0a29.dist-info/RECORD

@@ -0,0 +1,84 @@
+tests_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests_cli/test_client_script.py,sha256=_Wf8nKEfq6HEnfUQtwZvyICEmEa1TngyI_orPRQ7ZNQ,683
+tests_cli/test_example.py,sha256=0fw_v-lgZEacshWSDwLNyLMA1_xc48bKUGM3ll-n1L0,146
+tests_cli/test_node_cli.py,sha256=jM-nZkcvdEwwHVgQi8C7cYAbTJOzVmFl60MFXYVH9ig,16798
+tests_cli/test_server_cli.py,sha256=i0XBybUPn0_ACOHBi8d6vFETut7szz3Zt8ttmZhWVPc,6545
+tests_cli/test_wizard.py,sha256=ds2gJeBasQ06-nzqsPSSxrj-COe4pCLPgqrlBVkCXkw,5021
+vantage6/cli/__build__,sha256=NRNaqmzCOJG0DLPzeMU6F6ESchDOYOElzPA-_P2uxFg,2
+vantage6/cli/__init__.py,sha256=ZXbeQ_-g2-M4XYteWZkoO5lMFYhqjm5doQgGy1fq8i0,125
+vantage6/cli/_version.py,sha256=iDijqhgy5jzZ0LAyzW1LlXeeuMcHWMyg9D8xbXtV7Ck,696
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+vantage6/cli/configuration_manager.py,sha256=FV0RmiKmaGI2le8coUA4R5NTFUgPeph5XimxqgDhIsg,3332
+vantage6/cli/configuration_wizard.py,sha256=6UB4YwBlCjRT88bHgp6VeDFgQklAM2g2WXS10qmyhnY,18912
+vantage6/cli/globals.py,sha256=CxpxWXBLvAJR7st4-iRh95xbBZrn3qxKdbW3_7wmKY8,2245
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+vantage6/cli/algorithm/generate_algorithm_json.py,sha256=zwWtPVx_J2QtGHW9GnR3X95l0e3aP-zNASM6ADiVnrM,19983
+vantage6/cli/algorithm/update.py,sha256=WwAfTnq0kTOgePUsBzGoo1AJQqGMn82E9Bjk1wf61CQ,1338
+vantage6/cli/algostore/attach.py,sha256=0WzLnKigJAelPpL5EaWcnRuUyQzMSofrrZfEzwDIvSw,311
+vantage6/cli/algostore/files.py,sha256=r89VRixK_K-c44qseq58Aa2Dqf1wEf8yompQRN5AVu4,580
+vantage6/cli/algostore/list.py,sha256=xBCnwGbuWY_rrx6jrFX8JVAEFXh8GwqwicqpxMiaSa8,418
+vantage6/cli/algostore/new.py,sha256=ekqZ7_qCUtWs0QU6coo34thfkksHbCAYAD8nr0SKgO4,2147
+vantage6/cli/algostore/remove.py,sha256=ieQLpo2ZpblpPxaeRXdB7IO0DzTtURnveYQltW7TTSw,1643
+vantage6/cli/algostore/start.py,sha256=fse7beckD5bWtjQLQ8xRA_jeqsxM0cZjZo2_S0rYvSM,3160
+vantage6/cli/algostore/stop.py,sha256=Fqoj7W7NOW5nkvND5J2oSMqMD8knfD93fraN9KBSCmg,1836
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@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.45.1)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any