HEA Server Registry Microservice

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

The HEA Server Registry Microservice manages mappings of HEA Object types to the microservices for storing and retrieving them.

Version 1.13.1

• Bumped heaserver version to 1.61.1.

Version 1.13.0

• Bumped heaserver version to 1.61.0.
• Clear cache when updating a component.
• Use the /peopleviews and /groupviews endpoints for dropdowns.

Version 1.12.1

• Prevent 500 error when a user requests a settings object to which they don't have access.

Version 1.12.0

• Bumped heaserver version to 1.59.0.
• Added collection creation links.

Version 1.11.2

• Display in system menu and Display in user menu fields now have a default value.
• Corrected dropdown item order for Manages who can create objects.
• Added missing name attribute to registry component form template.
• Bumped heaserver version to 1.57.0.

Version 1.11.1

• Fixed sorting of collections.
• Request user and group lists sorted and filtered.
• Bumped heaserver version to 1.55.0.

Version 1.11.0

• Bumped heaserver version to 1.48.0.
• Added support for encrypted Mongo passwords.
• 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 1.10.2

• Fixed boolean mapping for manages_creators.

Version 1.10.1

• Fixed an issue keeping the Component resource_type_name property's value from appearing in form templates, and made the property read-write.
• Made the Manages who can create objects field in the registry component properties form writeable.

Version 1.10.0

• Bumped heaserver version to 1.35.0.
• Use new sort logic from heaserver 1.35, permitting sorting on components, collections, and properties by any attribute.
• Added sort-related query parameters to OpenAPI specs.

Version 1.9.0

• Removed preflight additions from version 1.8.0.
• Bumped heaserver version to 1.32.0.

Version 1.8.0

• Bumped heaserver version to 1.31.0.
• The heaobject.registry.Component class how has link_preflights and Resource.delete_preflight attributes.
• The heaobject.registry.Component template now includes the new link_preflights and delete_preflight attributes.

Version 1.7.0

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

Version 1.6.0

• Bumped heaserver version to 1.30.1.
• Improved properties metadata.
• Support heaobject.root.Permission.CREATOR permissions for heaobject.registry.Collection objects, as we will use those objects to create new objects.
• New heaserver.registry.service.RegistryServicePermissionGroup class that queries Mongo directly for whether the user can create objects of a given type.
• New heaserver.registry.service.RegistryMongo and RegistryMongoManager classes to allow using the new RegistryServicePermissionGroup class.
• Removed duplicate actions and added self actions where missing.
• Populate the heaobject.registry.Collection.display_in_system_menu, display_in_user_menu, and mime_type attributes from the registry components.

Version 1.5.1

• Bumped heaserver version to 1.28.1, fixing an issue with user group assignment checking.
• Removed duplicative automated tests.

Version 1.5.0

• Added group permissions support.

Version 1.4.0

• Added support for overhauled heaobject.storage.* classes.

Version 1.3.0

• Added support for new heaobject.activity.DesktopObjectSummaryView class.

Version 1.2.0

• Added support for Python 3.12.

Version 1.1.1

• Dependency upgrades for compatibility with heaserver-keychain 1.5.0.

Version 1.1.0

• Started using permissions for collections.

Version 1.0.4

• Fixed type hints.

Version 1.0.3

• Use the type display name in the properties card.
• Hide some other heaobject.registry.Collection attributes in the properties card.

Version 1.0.2

• When requesting desktop objects as a Collection+JSON document, add the permissions property to the document.
• Return the type_display_name attribute.

Version 1.0.1

• Made the collection object form template fields read-only, and added the type field.

Version 1

Initial release.

Runtime requirements

• Python 3.10 or 3.11

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 or 3.11: Download and install Python 3.10 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. 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.
• 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/components/ -Method GET -Headers @{'accept' = 'application/json'}`

In MacOS or Linux, the equivalent command is:

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

Packaging and releasing this project

See the RELEASING.md file for details.