Release Notes

For: uc-cdis/sheepdog

Notes since tag: 3.1.1

Notes to tag/commit: 3.2.0

Generated: 2021-09-01

New Features

Add option for isolation_level READ_COMMITTED. This addresses an error
which 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. (#351)
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. (#351)

Update uwsgi.ini and Dockerfile to support python dependency installs
(#351)
Update test suite (#351)
Add debug log when unable to parse JSON input (#354)
Handle TSV/CSV data for program/project creation (#354)
Adopt new base img with dd apm (#348)

Included python dependency updates in requirements.txt for
datamodelutils==1.0.0, dictionaryutils==3.2.0, gen3authz==0.4.0,
six>=1.15.0, py2neo, and google-crc32==1.1.2. (#351)
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.
(#351)
Included python dependency updates in dev-requirements.txt for
coverage==5.3.0 and codacy-coverage==1.3.11 (#351)
Bumps lxml from 4.4.2 to 4.6.3. (#342)