heaserver-organizations 1.10.2

a service for managing organization information for research laboratories and other research groups

HEA Server Organization

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

The HEA Server Organization is a service for managing organization information for research laboratories and other research groups.

Version 1.10.2

• Prevent "All collaborators must be removed from an account before removing it from the organization" error when updating an organization with collaborators with no associated account.

Version 1.10.1

• Write a type property for organization collaborators in the organization properties template.

Version 1.10.0

• Bumped heaserver version to 1.41.1.
• Added new collaborator info to endpoints.

Version 1.9.2

• Bumped heaserver to 1.37.1.

Version 1.9.1

• Bumped heaserver to 1.36.2.

Version 1.9.0

• Bumped heaserver to 1.35.0.
• Use new sort logic from heaserver 1.35.
• Added sort-related query parameters to OpenAPI specs.
• Fixed import statements in run-swaggerui.py.

Version 1.8.1

• Bumped heaserver version to 1.32.2 to correct a potential issue causing the microservice to fail to send messages to the message broker.

Version 1.8.0

• We now mark organizations with the new hea-container and hea-self-container rel values.
• Renamed the organizations/{id}/awsaccounts endpoint organizations/{id}/accounts, since that's what it was actually doing, and organizations are agnostic of the account type. The link from organization to account was updated to reflect this change.

Version 1.7.2

• Bumped heaserver version to 1.30.0.
• Removed duplicate user_shares and group_shares fields in the organization property metadata.

Version 1.7.1

• Bumped heaserver version to 1.28.1.

Version 1.7.0

• Added group permissions support.

Version 1.6.2

• Call the correct URL for removing a user from a group.

Version 1.6.1

• new links for org collection+json

Version 1.6.0

• New /organizations/{id}/recentlyaccessed endpoint.

Version 1.5.5

• Added support for python 3.12.

Version 1.5.4

• Fixed potential hang when listing an organization's accounts.

Version 1.5.3

• No user-visible changes. Updated to interoperate with heaserver-keychain 1.5.0.

Version 1.5.2

• Caching optimizations.

Version 1.5.1

• Invalidate cache when receiving collaborator changes from the message queue.

Version 1.5.0

• Added collaborator_ids attribute. The collaborator_ids attribute is altered via message queue messages.

Version 1.4.9

• Attempt to relink Credentials objects with their corresponding Volumes when saving an Organization.

Version 1.4.8

• Handle case where user who is an organization admin, manager, member, or PI has been deleted from keycloak.
• Omit system users from the membership editor form.

Version 1.4.7

• Fixed issue causing volumes and credentials for a new PI not to be created.

Version 1.4.6

• Fixed issue creating new credentials objects without a role when a user is added to an organization.

Version 1.4.5

• Fixed crash when reusing an existing volume and credentials when a user's organization membership has changed.

Version 1.4.4

• Return 400 status code when the user lacks permission to update permissions for an organization (those errors were ignored previously).
• Corrected permissions checking for organization managers and members.

Version 1.4.3

• Send the account ids and group id fields when submitting the members editor form.

Version 1.4.2

• Corrected heaobject.organization.Organization permissions.

Version 1.4.1

• Generate the correct name attribute for heaobject.keychain.AWSCredentials objects.

Version 1.4.0

• Changing organization members, managers, admins, and PI now changes the users' volumes and credentials objects to match.
• The admin, manager, and member lists now omit system users.

Version 1.3.0

• Display type display name in properties card, and return the type display name from GET calls.

Version 1.2.0

• Improved performance accessing an organization's AWS accounts.
• heaobject.organization.Organization objects now have an accounts attribute that mirrors the contents of the existing aws_account_ids attribute and will support other heaobject.account.Account subclasses in the future.

Version 1.1.0

• Pass desktop object permissions back to clients.

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.
• 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.
• 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/organizations/ -Method GET -Headers @{'accept' = 'application/json'}`

In MacOS or Linux, the equivalent command is:

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

Packaging and releasing this project

See the RELEASING.md file for details.