Arvados

There are several legacy tables "humans" "specimens" and "traits". These were added extremely early on with the best intentions of supporting the PGP use case but as far as I know they have never used for their intended purpose. They should be deprecated and removed to de-clutter the API.

1. Announce deprecation/removal in future version (already done)
2. A few integration tests use these APIs because they are generic resources with no business logic. These tests need to be updated to use a different resource or otherwise perform test a different way.
3. Delete models, controllers, tests, and routes from API server
4. Delete from documentation

These should not appear in the discovery document or the auto-generated python docs. The auto-generated SDKs (e.g. the R SDK) should also be updated.

We are also dropping the hosting git repository support (the "repositories" table). This means we can delete arvados/services/githttpd.

We would also like to remove and stop publishing anything related to the jobs API, e.g. "jobs" and "job_tasks", "pipeline_instances", "pipeline_templates", "nodes".

We should also get rid of the "keep_disks" table.

We should remove some unused fields from "api_client_authorization" response: default_owner_uuid, api_client_id, user_id (the _id fields may need to remain internally but should not be published by the API because they are not usable with any other API calls).

We should remove redundant resource methods from the Discovery Document (the Python and R autogenerated APIs already filter these out, so they are undocumented and nobody should be using them):

• "show" (synonym for "get")
• "index" (synonym for "list")
• "destroy" (synonym for "delete")

There's a "Managed" section under SLURM that has options related to the obsolete slurm-on-cloud configuration.

Another thing to get rid of: support for legacy component-specific config files.

Config options to remove:

Mail.IssueReporterEmailFrom, Mail.IssueReporterEmailTo -- only used by Workbench1 mailers

Mail.EmailFrom -- also only used by Workbench1 mailers

Mail.MailchimpAPIKey, Mail.MailchimpListID -- seem to be tied to a long lost arvados-mailchimp-plugin that we don't use and can't locate

If we delete all of these, the only option left is "SendUserSetupNotificationEmail" which should really migrate to the "Users" section where all the actually-in-use user notification mail options are located.