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SODAR Taskflow Changelog

Changelog for the SODAR Taskflow service.

v0.6.2 (2022-07-20)

Changed

  • Upgrade to python-irodsclient v1.1.3 (#93, #97)
  • Upgrade general dependencies (#94)
  • Drop support for Python <3.8, add support for v3.10 (#95)
  • Upgrade to Python v3.8 in Docker build (#95)
  • Upgrade to black v22.3.0

Fixed

  • Uncaught exception in SetCollectionMetadataTask (#96)

v0.6.1 (2022-02-02)

Changed

  • Upgrade to python-irodsclient v1.1.0 (#91)
  • Allow setting DEBUG in production config (#92)
  • Ignore cache in build-docker.sh

v0.6.0 (2021-12-14)

Added

  • LABEL AND MAINTAINER in Dockerfile (#77)
  • Replica checksum validation in BatchValidateChecksumsTask (#78)
  • Support for extra data in SetLandingZoneStatusTask (#81)
  • status and flow_name arguments for RevertLandingZoneFailTask (#86)
  • flow_name argument for SetLandingZoneStatusTask
  • BatchCheckFilesTask for checking file and MD5 checksum presence (#63)
  • iRODS environment setup via TASKFLOW_IRODS_ENV_OVERRIDE (#90)

Changed

  • Improve iRODS exception logging (#34)
  • Upgrade to python-irodsclient v1.0.0 (#79)
  • Update docker build for ghcr.io
  • Display user name instead of path in SetAccessTask revert
  • Set zone status to NOT CREATED on landing_zone_create failure (#86)
  • Improve RevertLandingZoneFailTask info messages
  • Improve iRODS task exception messages
  • Change test config log level to CRITICAL

Fixed

  • Redundant info in BatchValidateChecksumsTask error logging (#80)
  • Errors in landing_zone_move zone status messages (#82)
  • landing_zone_create script user access task exception not resulting in revert (#85)
  • _raise_irods_exception() helper

Removed

  • set_script_user_access() helper, use SetAccessTask instead (#85)
  • IRODS_ENV_PATH support (#90)

v0.5.0 (2020-06-07)

Added

  • Support for TASKFLOW_IRODS_PROJECT_ROOT setting (#69)
  • data_delete flow for deleting data (#67)
  • Support for public_guest_access field in project updates (#70)
  • public_access_update for setting public read access to collections (#71)
  • GitHub CI using GitHub Actions (#74)

Changed

  • Upgrade project requirements(#66, #68, #72)
  • Unify collection naming (#58)
  • Update Docker setup
  • Update test cleanup

Fixed

  • project_description field required in project_update (#64)
  • Disallowed empty values not sanitized in SetCollectionMetadataTask (#64)
  • Invalid env variable OMICS_TASKFLOW_SETTINGS in GitLab CI (#76)

v0.4.0 (2020-04-28)

Added

  • Flow role_update_irods_batch for updating user roles in iRODS (#60)
  • Inherited category owners into iRODS user groups in project_create (#59)
  • Bulk updating of user roles in project_update (#61)
  • iRODS task RemoveDataObjectTask

Changed

  • Upgrade project requirements (#54)

Fixed

  • Crash with Networkx > v2.2 (#52)
  • Logging on Flask v1.1+ (#62)

v0.3.4 (2020-01-06)

Added

  • Supply optional iRODS options in environment file (#56)
  • TASKFLOW_IRODS_ENV_PATH settings variable (#56)

Changed

  • Refactor Python2-style super() calls (#53)
  • Upgrade to python-irodsclient v0.8.2 (#57)

Fixed

  • Crash caused by networkx==2.4 installed by taskflow (#52)
  • Unhandled Tooz connection exception (#46)

v0.3.3 (2019-07-05)

Changed

  • Improve BatchValidateChecksumsTask status messages (#50)

Fixed

  • Modified owner not created at iRODS in project_update (#49)

Removed

  • Unused ValidateDataObjectChecksumTask

v0.3.2 (2019-02-25)

Added

  • Flake8 and Black configuration and CI checks (#42)

Changed

  • Prettify Tooz lock status logging (#33)
  • Upgrade Python package requirements (#44)
  • Update service to work with Flask v1.0+ (#45)
  • Upgrade minimum Python version requirement to 3.6
  • Format code with Black (#41)
  • Code cleanup and refactoring (#42)

Fixed

  • Checksum validation failure on tab-formatted .md5 files (#40)
  • Wrong landing zone status info for "validate only" mode (#43)

Removed

  • Unnecessary byte encoding in Tooz lock API (#33)

v0.3.1 (2018-12-19)

Added

  • Support for additional iRODS test server (sodar_core#67)
  • Dotenv configuration (#37)
  • Use TASKFLOW_SODAR_SECRET variable for securing connections (sodar_core#46)

Removed

  • Unneeded utility/test_local.sh script

v0.3.0 (2018-10-26)

Added

  • More informative exception message for CAT_NAME_EXISTS_AS_DATAOBJ in BatchMoveDataObjectsTask

Changed

  • Rebrand site as SODAR Taskflow (#36)
  • Expect sodar_url parameter instead of omics_url for SODAR Core compatibility (#35)

Fixed

  • Missing exception __str__() detection in _raise_irods_exception()

v0.2.1 (2018-08-24)

Added

  • Workaround for iRODS ticket issue in the bih_proteomics_smb case (omics_data_mgmt#297)
  • Proper exception reporting for AddUserToGroupTask (#4)
  • Option for validating only in landing_zone_move (omics_data_mgmt#333)

Changed

  • Modify iRODS exception raising in attempt to catch exception name (#34)

Fixed

  • Project lock timeouts in async flows due to initiating coordinator in the wrong process (#32)

v0.2.0 (2018-07-03)

Added

  • Async support for landing_zone_delete (omics_data_mgmt#228)
  • Option for not requiring lock by setting flow.require_lock to False (omics_data_mgmt#231)
  • Support for landing zone configuration

Fixed

  • Configuration in utility/run_prod.sh
  • Concurrent requests failed in debug mode, now using multiple processes
  • Failure in acquiring lock was not correctly reported in async mode (omics_data_mgmt#235)
  • Project update failure if readme is empty (omics_data_mgmt#251)

Removed

  • Support for omics_tasks.RemoveLandingZoneTask as it's no longer needed (omics_data_mgmt#228)

v0.2.0b (2018-06-05)

Added

  • Project settings modification in project creation/update
  • Helper functions for building directory paths in irods_utils
  • This changelog :)

Changed

  • Use UUIDs instead of pk:s when referring to omics_data_mgmt objects (#14)
  • Modify SODAR Taskflow API URLs
  • Improve SODAR API error reporting
  • Upgrade to python-irodsclient 0.7.0 (#10)
  • Upgrade taskflow and tooz
  • Readme rewritten and converted to rst
  • Configure sample and landing zone directory names in settings
  • Flow sheet_delete: also delete landing zones
  • Refactor get_project_path()
  • Update landing_zone_create for assay specific zones (#15)
  • Update landing_zone_delete (#15)
  • Modify run_prod.sh to run Gunicorn with production settings
  • Project user groups are now in form of omics_project_{UUID}
  • Add proper logging
  • Use gevent in production mode (#26)
  • Upgrade to gunicorn==19.8.1

Removed

  • Flynn references removed as deploying via Flynn is no longer supported
  • Redundant debug printouts (all now going to logger)

Fixed

  • Data object read access was left for landing zone user account in sample data (#19)
  • Failure in landing_zone_move raised NOT CREATED instead of FAILED (#20)
  • Missing project_readme param in UpdateProjectTask (#23)
  • Creating an empty directory if uploading files in landing zone root (#24)

v0.1-PROTOTYPE (2018-04-13)

  • Tagged to freeze the version used with the original omics_data_access prototype