Bump cryptography

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 5.1.3

Notes to tag/commit: 8045c96

Generated: 2024-02-12

Dependency Updates

• cryptography to 42.0.2, poetry to 1.7.1 (#406)

Upgrade pyyaml

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 5.1.2

Notes to tag/commit: 359c764

Generated: 2023-11-17

Dependency Updates

• PyYAML to >=5.4.1 (#404)
• gen3dictionary to >= 2.0.3 (#404)
• dictionaryutils to >=3.4.10 (#404)

5.1.2

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 5.1.0

Notes to tag/commit: d2893b1

Generated: 2023-11-14

Bug Fixes

• Fix validation issue when submitting null values allowed by a oneOf/anyOf
  dictionary property definition (#398)
• (#398)

Improvements

• Code coverage reported to coveralls through GH action. (#401)
• Replaces codacy badge with coveralls (#401)
• Remove unused oauth2 blueprint and its settings and dependencies (#402)
• fix(travis): remove travis CI, replace with GH Actions (#400)
• Fix Swagger docs: add /v0/submission prefix (#395)
• JSON export returns JSON arrays instead of comma-delimited strings (#394)
• Log actual grant_read_permissions_to_graph errors (#388)

Dependency Updates

• Flask to 2.3.3 (#403)
• Remove cdis_oauth2client dependency (#402)
• remove cryptography, update requests & urllib3, fix other packages to
  ensure successful dependency resolution (#399)

Python 3.9

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 5.0.1

Notes to tag/commit: 5.1.0

Generated: 2023-02-02

Improvements

• The unit tests have been refactored so that some of the duplicated setup is
  now shared (#387)

Dependency Updates

• Python 3.9 (#387)
• indexclient to 2.1.1 (#387)
• Use Poetry for dependency management. Update and clean up dependencies. Set
  more flexible dependency versions. (#387)

Deployment Changes

• Sheepdog does not rely on configuration files in the cloud-automation
  repository anymore. The Sheepdog configuration files are in the Sheepdog
  repository. (#387)

dep updates

Release Notes

For: uc-cdis/sheepdog
Notes since tag: 5.0.0
Notes to tag/commit: b50fde4

Generated: 2023-01-23

Improvements

• Removing Veracode scanning pipeline (#373)
• Removing Veracode scanning pipeline (#372)

Dependency Updates

• upgrade cryptography to latest version (and other necessary deps) (#381)
• boto to 2.39.0 (#376)

Format validation and bug fixes

Release Notes

For: uc-cdis/sheepdog
Notes since tag: 3.3.0
Notes to tag/commit: d52b058
Generated: 2022-09-01

NOTE: For some reason I see we went from 4.x -> 3.x in the semantic releases in the past, rather than up to 5.x. I'm jumping up to 5.0.0 with this breaking change to clearly tag this as the latest

New Features

• Validate jsonschema format during submission (#363)

Breaking Changes

• Sheepdog now validates formats. If your dictionary uses formats and you
  have existing data or submission pipelines that do not respect these
  formats, this might be a breaking change (#363)

Bug Fixes

• Fix issue where arrays of ints gets converted to array of floats (#371)
• update to latest base image to avoid issue with dockerrun (#361)

Improvements

• Local Development notes and sample usage (#350)
• Split "use SSL" and "isolation level" unit tests into their own file. The
  previous parametrization caused the tests to take 30+ min to run, because
  all tests that use the pg_driver fixture were ran 12 times (#364)

Dependency Updates

• Upgrade Flask-Cors to version 3.0.9 or higher. (#365)
• Upgrade urllib3 to version 1.26.5 or higher. (#365)
• gen3datamodel to 3.1.0 (#363)

3.3.0

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 3.2.2

Notes to tag/commit: 3.3.0

Generated: 2021-11-02

Bug Fixes

• Fix export for non-string array values introduced in versions 3.2.0 /
  2021.10 (#360)

Dependency Updates

• Use new Python base image (now: Debian, before: Alpine) (#358)

3.2.2

Release Notes

For: uc-cdis/sheepdog

Notes since tag: 3.2.1

Notes to tag/commit: d0cfeb7

Generated: 2021-10-26

Improvements

• Increased uWSGI timeout to 10 minutes (600 seconds) (#357)
• Add example Azure DevOps pipeline and documentation (#353)

update base image

Release Notes

For: uc-cdis/sheepdog
Notes since tag: 3.2.0
Notes to tag/commit: e3409d0
Generated: 2021-09-08

Improvements

• update to latest python base image (#356)

3.2.0

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

• Update for PostgreSQL SSL support (#351)

Bug Fixes

• 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)

Improvements

• 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)

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, 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)