heaserver-data-adapters 1.0.0a16

The HEA data adapter service.

HEA Server Data Adapters Microservice

Research Informatics Shared Resource, Huntsman Cancer Institute, Salt Lake City, UT

The HEA Data Adapters Microservice provides access to data files and databases.

Version 1

Initial release.

Runtime requirements

• Python 3.8

Development environment

Build requirements

• Any development environment is fine.
• On Windows, you also will need:
  • Build Tools for Visual Studio 2019, found at https://visualstudio.microsoft.com/downloads/. Select the C++ tools.
  • git, found at https://git-scm.com/download/win.
• On Mac, Xcode or the command line developer tools is required, found in the Apple Store app.
• Python 3.8: Download and install Python 3.8 from https://www.python.org, and select the options to install for all users and add Python to your environment variables. The install for all users option will help keep you from accidentally installing packages into your Python installation's site-packages directory instead of to your virtualenv environment, described below.
• Create a virtualenv environment using the python -m venv <venv_directory> command, substituting <venv_directory> with the directory name of your virtual environment. Run source <venv_directory>/bin/activate (or <venv_directory>/Scripts/activate on Windows) to activate the virtual environment. You will need to activate the virtualenv every time before starting work, or your IDE may be able to do this for you automatically. Note that PyCharm will do this for you, but you have to create a new Terminal panel after you newly configure a project with your virtualenv.
• From the project's root directory, and using the activated virtualenv, run pip install wheel followed by pip install -r requirements_dev.txt. Do NOT run python setup.py develop. It will break your environment.

Running tests

Run tests with the pytest command from the project root directory.

Running integration tests

• Install Docker
• On Windows, install pywin32 version >= 223 from https://github.com/mhammond/pywin32/releases. In your venv, make sure that include-system-site-packages is set to true.

Trying out the APIs

This microservice has Swagger3/OpenAPI support so that you can quickly test the APIs in a web browser. Do the following:

• Install Docker, if it is not installed already.
• Run the run-swaggerui.py file in your terminal. This file contains some test objects that are loaded into a MongoDB Docker container.
• Go to http://0.0.0.0:8080/docs in your web browser.

Versioning

Use semantic versioning as described in https://packaging.python.org/guides/distributing-packages-using-setuptools/#choosing-a-versioning-scheme. In addition, while development is underway, the version should be the next version number suffixed by .dev.

Version tags in git

Version tags should follow the format heaserver-data-adapters-<version>, for example, heaserver-data-adapters-1.0.0.

Uploading to an index server

The following instructions assume separate stable and staging indexes. Numbered releases, including alphas and betas, go into the stable index. Snapshots of works in progress go into the staging index. Thus, use staging to upload numbered releases, verify the uploaded packages, and then upload to stable.

From the project's root directory:

1. For numbered releases, remove .dev from the version number in setup.py, tag it in git to indicate a release, and commit to version control. Skip this step for developer snapshot releases.
2. Run python setup.py clean --all sdist bdist_wheel to create the artifacts.
3. Run twine upload -r <repository> dist/<wheel-filename> dist/<tarball-filename> to upload to the repository. The repository name has to be defined in a twine configuration file such as $HOME/.pypirc.
4. For numbered releases, increment the version number in setup.py, append .dev to it, and commit to version control with a commit message like, "Prepare for next development iteration."