New Features

• Update for PostgreSQL SSL support

Breaking Changes

Bug Fixes

• Add option for isolation_level READ_COMMITTED. This error occurs when there's competing transactions in the sheepdog database, for example, when using multiple workers in uwsgi which are trying to reach a shared resource in sheepdog_db.
  The conflict occurs after submitting multiple requests to sheepdog using the gen3sdk for python (see https://github.com/uc-cdis/gen3sdk-python/blob/master/gen3/submission.py#L187) as part of populating the data dictionary with metadata. In this case, it looks like the race condition mentioned here https://github.com/uc-cdis/cloud-automation/blob/1f9cbb52cecf449a5ad76f984fe0dda449d924d3/kube/services/jobs/gdcdb-create-job.yaml#L48 is occurring. This is a workaround to use isolation_level of READ_COMMITTED within sheepdog.

Improvements

• Local Development notes and sample usage
• Address sphinx-based docs generation.
• Add example Azure DevOps pipeline and documentation
• Update uwsgi.ini and Dockerfile to support python dependency installs
• Update test suite

Dependency updates

• Included python dependency updates in requirements.txt for datamodelutils==1.0.0, dictionaryutils==3.2.0, gen3authz==0.4.0, six>=1.15.0, and py2neo.

Note that dictionaryutils==3.4.0 is the current sheepdog python dependency but is not available for download from pypi (at least with a wsl / windows release). The lower version 3.2.0 is a workaround.

• Included python dependency updates in dev-requirements.txt for coverage==5.3.0 and codacy-coverage==1.3.11

Deployment changes