vantage6 3.0.0__tar.gz → 4.13.6__tar.gz

vantage6-4.13.6/PKG-INFO

@@ -0,0 +1,238 @@
+Metadata-Version: 2.4
+Name: vantage6
+Version: 4.13.6
+Summary: vantage6 command line interface
+Home-page: https://github.com/vantage6/vantage6
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: click==8.1.3
+Requires-Dist: colorama==0.4.6
+Requires-Dist: copier==9.11.3
+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: questionary==2.1.1
+Requires-Dist: rich==13.5.2
+Requires-Dist: schema==0.7.5
+Requires-Dist: SQLAlchemy==1.4.46
+Requires-Dist: vantage6-common==4.13.6
+Requires-Dist: vantage6-client==4.13.6
+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>
+  <a href="https://vantage6.ai"><img src="https://github.com/IKNL/guidelines/blob/master/resources/logos/vantage6.png?raw=true" alt="vantage6" width="350"></a>
+</h1>
+
+<h3 align=center> A Privacy Enhancing Technology (PET) Operations platform</h3>
+<h3 align="center">
+
+<!-- Badges go here-->
+
+[![Release](https://github.com/vantage6/vantage6/actions/workflows/release.yml/badge.svg)](https://github.com/vantage6/vantage6/actions/workflows/release.yml)
+[![PyPI vantage6](https://badge.fury.io/py/vantage6.svg)](https://badge.fury.io/py/vantage6)
+[![Unittests](https://github.com/vantage6/vantage6/actions/workflows/unit_tests.yml/badge.svg)](https://github.com/vantage6/vantage6/actions/workflows/unit_tests.yml)
+[![Coverage Status](https://coveralls.io/repos/github/vantage6/vantage6/badge.svg?branch=main)](https://coveralls.io/github/vantage6/vantage6?branch=main)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/2e60ac3b3f284620805f7399cba317be)](https://app.codacy.com/gh/vantage6/vantage6/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+[![DOI](https://zenodo.org/badge/492818831.svg)](https://zenodo.org/badge/latestdoi/492818831)
+[![Discord](https://img.shields.io/discord/643526403207331841)](https://discord.gg/yAyFf6Y)
+[![Research software directory](https://img.shields.io/badge/rsd-vantage6-deepskyblue)](https://research-software-directory.org/software/vantage6)
+
+
+</h3>
+
+<p align="center">
+  <a href="#books-quickstart">Quickstart</a> •
+  <a href="#project-structure">Project structure</a> •
+  <a href="#gift_heart-join-the-community">Join the community</a> •
+  <a href="#scroll-license">License</a> •
+  <a href="#black_nib-code-of-conduct">Code of conduct</a> •
+  <a href="#black_nib-references">References</a>
+</p>
+
+---
+
+This repository is contains all the **vantage6** infrastructure source code. The **vantage6** technology enables to manage and deploy privacy enhancing technologies like Federated Learning (FL) and Multi-Party Computation (MPC). Please visit our [website](https://vantage6.ai) to learn more!
+
+You can find more (user) documentation at [readthedocs](https://docs.vantage6.ai). If you have any questions, suggestions or just want to chat about federated learning: join our [Discord)](https://discord.gg/yAyFf6Y) channel.
+
+## Infrastructure overview
+
+![Vantage6 architecture overview](docs/images/overview-infrastructure.png)
+
+_A High level overview of the vantage6 infrastructure. Vantage6 has both a
+client-server and peer-to-peer architecture. The client is used by the researcher to
+create (PET) computation requests. It is also used to manage users, organizations and
+collaborations. The server contains users, organizations, collaborations, tasks and
+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._
+
+## :books: Quickstart
+
+### Requirements
+
+The **vantage6** infrastructure is delivered in Docker images. To run these images, you
+need to have [Docker](https://docs.docker.com/get-docker/) installed. To install the
+latest version of the vantage6 CLI, you need to have
+[Python](https://www.python.org/downloads/), we recommend using an environment manager
+like [mini-conda](https://docs.conda.io/en/latest/miniconda.html).
+
+Install the latest version of the vantage6 CLI by using:
+
+```bash
+pip install vantage6
+```
+
+This install the `v6` commands, which allows you to manage your nodes and servers. To view all available options, run:
+
+```bash
+v6 --help
+```
+
+For example you can create a local test setup by using:
+
+```bash
+v6 dev create-demo-network
+```
+
+This creates a local network with a server and two nodes. You can start the network by running:
+
+```bash
+v6 dev start-demo-network
+```
+
+This will start the server and nodes in the background. You can view the logs by running:
+
+```bash
+# View node logs
+v6 node attach
+
+# View server logs
+v6 server attach
+```
+
+From here you can use the [vantage6-client](https://pypi.org/project/vantage6-client)
+to interact with the server. The demo network has a pre-configured organization with
+the following credentials:
+
+- Username: `dev_admin`
+- Password: `password`
+
+For example, you can create a new organization by running:
+
+```python
+from vantage6.client import Client
+
+client = Client('http://127.0.0.1', 7601, '/api', log_level='debug')
+client.authenticate('dev_admin', 'password')
+client.setup_encryption(None)
+
+client.organization.create(
+    name='My organization',
+    address1='My address',
+    address2='My address',
+    zipcode='1234AB',
+    country='The Netherlands',
+    domain='my-organization.com'
+)
+```
+
+You can find more (user) documentation at [readthedocs](https://docs.vantage6.ai)
+
+## Project structure
+
+### PYPI packages
+
+This repository is home to 6 PyPi packages:
+
+- [vantage6](https://pypi.org/project/vantage6) -> _CLI for managing node and server instances_
+- [vantage6-client](https://pypi.org/project/vantage6-client) -> _Python client for interacting with the vantage6-server_
+- [vantage6-algorithm-tools](https://pypi.org/project/vantage6-algorithm-tools) -> _Python tools to facilitate algorithm development_
+- [vantage6-node](https://pypi.org/project/vantage6-node) -> _Node application package_
+- [vantage6-server](https://pypi.org/project/vantage6-server) -> _Server application package_
+- [vantage6-algorithm-store](https://pypi.org/project/vantage6-algorithm-store) -> _Algorithm store application package_
+- [vantage6-common](https://pypi.org/project/vantage6-common) -> _Package with common vantage6 functions_
+- [vantage6-backend-common](https://pypi.org/project/vantage6-backend-common) -> _Package with functions common to central server and algorithm store_
+
+**Note that when using vantage6 you do not install the _server_ and _node_ packages. These are delivered to you in Docker images.**
+
+This repository also hosts the code for the vantage6 user interface (UI). The UI
+is an Angular web application that can be used to interact with the vantage6 server
+easily.
+
+### Docker images
+
+The vantage6 infrastructure is delivered in Docker images. All Docker images are stored
+in our private [Harbor](https://goharbor.io/) registry. The most important images are:
+
+- `harbor2.vantage6.ai/infrastructure/node:VERSION` -> _Node application Docker image_
+- `harbor2.vantage6.ai/infrastructure/server:VERSION` -> _Server application Docker image_
+- `harbor2.vantage6.ai/infrastructure/ui:VERSION` -> _User interface Docker image_
+- `harbor2.vantage6.ai/infrastructure/algorithm-store:VERSION` -> _Algorithm store Docker image_
+
+with `VERSION` being the full semantic version of the vantage6 infrastructure, e.g.
+`4.0.0` or `4.1.0rc0`.
+
+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:
+
+- `harbor2.vantage6.ai/infrastructure/algorithm-base:MAJOR.MINOR` -> _Base image for algorithm development_
+- `harbor2.vantage6.ai/infrastructure/algorithm-ohdsi-base:MAJOR.MINOR` -> _Extended algorithm base image for OHDSI algorithm development_
+
+## :gift_heart: Join the community!
+
+We hope to continue developing, improving, and supporting **vantage6** with the help of 
+the federated learning community. If you are interested in contributing, first of all, 
+thank you! Second, please take a look at our 
+[contributing guidelines](https://docs.vantage6.ai/en/main/devops/contribute.html) 
+and our [code of conduct](CODE_OF_CONDUCT.md).
+
+<a href="https://github.com/vantage6/vantage6/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=vantage6/vantage6" />
+</a>
+
+## :scroll: License
+
+This project is licensed under the Apache License 2.0 - see the [LICENSE](LICENSE) file for details.
+
+## :black_nib: Code of Conduct
+
+Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). **By participating in any way in this project you agree to abide by its terms.**
+
+## :black_nib: References
+
+If you are using **vantage6**, please cite this repository as well as the accompanying papers as follows:
+
+> - F. Martin, M. Sieswerda, H. Alradhi, et al. vantage6. Available at https://doi.org/10.5281/zenodo.7221216. Accessed on MONTH, 20XX.
+> - A. Moncada-Torres, F. Martin, M. Sieswerda, J. van Soest, G. Gelijnse. VANTAGE6: an open source priVAcy preserviNg federaTed leArninG infrastructurE for Secure Insight eXchange. AMIA Annual Symposium Proceedings, 2020, p. 870-877. [[BibTeX](https://arturomoncadatorres.com/bibtex/moncada-torres2020vantage6.txt), [PDF](https://vantage6.ai/vantage6/)]
+> - D. Smits\*, B. van Beusekom\*, F. Martin, L. Veen, G. Geleijnse, A. Moncada-Torres, An Improved Infrastructure for Privacy-Preserving Analysis of Patient Data, Proceedings of the International Conference of Informatics, Management, and Technology in Healthcare (ICIMTH), vol. 25, 2022, p. 144-147. [[BibTeX](https://arturomoncadatorres.com/bibtex/smits2022improved.txt), [PDF](https://ebooks.iospress.nl/volumearticle/60190)]
+
+---
+
+<p align="center">
+  <a href="https://vantage6.ai">vantage6.ai</a> •
+  <a href="https://discord.gg/yAyFf6Y">Discord</a> •
+  <a href="https://vantage6.discourse.group/">Discourse</a> •
+  <a href="https://docs.vantage6.ai">User documentation</a>
+</p>

vantage6-4.13.6/setup.py

@@ -0,0 +1,79 @@
+import codecs
+import os
+from codecs import open
+from os import path
+from pathlib import Path
+
+from setuptools import find_namespace_packages, setup
+
+# get current directory
+here = Path(path.abspath(path.dirname(__file__)))
+parent_dir = here.parent.absolute()
+
+# get the long description from the README file
+with codecs.open(path.join(parent_dir, "README.md"), encoding="utf-8") as f:
+    long_description = f.read()
+
+# Read the API version from disk. This file should be located in the package
+# folder, since it's also used to set the pkg.__version__ variable.
+version_path = os.path.join(here, "vantage6", "cli", "_version.py")
+version_ns = {"__file__": version_path}
+with open(version_path) as f:
+    exec(f.read(), {}, version_ns)
+
+
+# setup the package
+setup(
+    name="vantage6",
+    version=version_ns["__version__"],
+    description="vantage6 command line interface",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/vantage6/vantage6",
+    packages=find_namespace_packages(),
+    python_requires=">=3.10",
+    install_requires=[
+        "click==8.1.3",
+        "colorama==0.4.6",
+        "copier==9.11.3",
+        "docker==7.1.0",
+        "ipython==8.10.0",
+        "jinja2==3.1.6",
+        "pandas>=1.5.3",
+        "questionary==2.1.1",
+        "rich==13.5.2",
+        "schema==0.7.5",
+        "SQLAlchemy==1.4.46",
+        f"vantage6-common == {version_ns['__version__']}",
+        f"vantage6-client == {version_ns['__version__']}",
+    ],
+    extras_require={
+        "dev": [
+            "coverage==6.4.4",
+            "black",
+            "pre-commit",
+        ]
+    },
+    package_data={
+        "vantage6.cli": [
+            "__build__",
+            "rabbitmq/rabbitmq.config",
+            "template/node_config.j2",
+            "template/server_config.j2",
+            "template/server_import_config.j2",
+            "template/algo_store_config.j2",
+            "dev/data/olympic_athletes_2016.csv",
+            "dev/data/km_dataset.csv",
+            "prometheus/prometheus.yml",
+        ],
+    },
+    entry_points={
+        "console_scripts": [
+            "v6=vantage6.cli.cli:cli_complete",
+            # TODO v5+ remove vnode/vserver/vdev aliases (?)
+            "vnode=vantage6.cli.cli:cli_node",
+            "vserver=vantage6.cli.cli:cli_server",
+            "vdev=vantage6.cli.cli:cli_dev",
+        ]
+    },
+)

vantage6-4.13.6/tests_cli/test_client_script.py

@@ -0,0 +1,23 @@
+from click import UsageError
+from vantage6.cli.test.client_script import cli_test_client_script
+
+import click
+import unittest
+
+
+class TestScriptTest(unittest.TestCase):
+    def test_script_incorrect_usage(self):
+        ctx = click.Context(cli_test_client_script)
+
+        with self.assertRaises(UsageError):
+            ctx.invoke(
+                cli_test_client_script,
+                script="path/to/script.py",
+                task_arguments="{'my_arg': 1}",
+            )
+
+        with self.assertRaises(UsageError):
+            ctx.invoke(
+                cli_test_client_script,
+                task_arguments="not_a_json",
+            )

{vantage6-3.0.0/tests → vantage6-4.13.6/tests_cli}/test_example.py

@@ -2,7 +2,6 @@ import unittest
 
 
 class ExampleTest(unittest.TestCase):
-
     def test_example(self):
         self.assertTrue(True)
         self.assertFalse(False)