HEA Volumes Microservice

Comprehensive Oncology Data and Engineering Shared Resource (CODE), Huntsman Cancer Institute, Salt Lake City, UT

The HEA Volumes Microservice.

Version 1.9.2

• CI/CD.
• Bumped heaserver version to 1.72.0 and heaobject to 1.51.1.
• Bumped python version in Dockerfile to 3.12.15.

Version 1.9.1

• Bumped heaserver version to 1.61.1.

Version 1.9.0

• Bumped heaserver version to 1.61.0.
• Use the /peopleviews and /groupviews endpoints for dropdowns.

Version 1.8.2

• Bumped heaserver version to 1.59.0.

Version 1.8.1

• Bumped heaserver version to 1.55.0.
• Dropdowns are now sorted.
• Request only required attributes in template form dropdowns.

Version 1.8.0

• Bumped heaserver version to 1.48.0.
• Added support for encrypted Mongo passwords.

Version 1.7.0

• Bumped heaserver version to 1.45.1.
• New startup.py module to initialize logging before importing any third-party libraries.
• New optional -e/--env command-line argument for setting the runtime environment (development, staging, or production). Logging is now configured based on this setting, unless the older -l/--logging argument is provided. The default value is development.
• Logs are now scrubbed.
• Added log files to .gitignore.

Version 1.6.0

• Bumped heaserver version to 1.43.0.
• Updated tests for heaobject.volume.Volume attribute changes.
• Updated form templates for attribute changes.

Version 1.5.2

• Bumped heaserver version to 1.32.1. The super_admin_default_permissions attribute now is an empty list.

Version 1.5.1

• Bumped heaserver version to 1.32.0.
• Send user and group permissions and the super-admin default permissions in the properties template.

Version 1.5.0

• We now mark volumes with the new hea-container and hea-self-container rel values.

Version 1.4.1

• Bumped heaserver version to 1.30.1.

Version 1.4.0

• Added python 3.12 support.
• Fixed URL for retrieving credentials objects for the properties form.
• Added support for group permissions.

Version 1.3.0

• We now pass the type_display_name property in volume Collection+JSON templates.
• Caching optimizations.

Version 1.2.0

• Hid some attributes from the heaobject.volume.Volume properties card.
• Added account_id attribute to the heaobject.volume.Volume properties card.
• Removed the type name filter from volume queries. We now use heaobject.account.AccountView ids for the account id filter.

Version 1.1.0

• Support filtering volumes by account id and type name.

Version 1.0.2

• Improved performance.

Version 1.0.1

• Improved performance.

Version 1

Initial release.

Runtime requirements

• Python 3.10, 3.11, or 3.12.

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 3.10, 3.11, or 3.12: Download and install Python 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.
• Upgrade pip to version 21.1.2 or greater with python -m pip install --upgrade pip.
• 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 -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. To improve performance, run tests in multiple processes with pytest -n auto.

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.
• Have a heaserver-registry docker image in your Docker cache. You can generate one using the Dockerfile in the heaserver-registry project.
• Have a heaserver-folders docker image in your Docker cache. You can generate one using the Dockerfile in the heaserver-folders project.
• 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://127.0.0.1:8080/docs in your web browser.

Once run-swaggerui.py is running, you can also access the APIs via curl or other tool. For example, in Windows PowerShell, execute:

Invoke-RestMethod -Uri http://localhost:8080/volumes/ -Method GET -Headers @{'accept' = 'application/json'}`

In MacOS or Linux, the equivalent command is:

curl -X GET http://localhost:8080/volumes/ -H 'accept: application/json'

Packaging and releasing this project

See the RELEASING.md file for details.