Changelog¶
0.7.16 (2024-09-20)¶
- Fixed circus dependencies
0.7.15 (2024-09-19)¶
- Added prompt to confirm overwrite if qa-report already exists
0.7.14 (2022-03-09)¶
- Updated Datomic download source to Wormbase bucket (datomic free download no longer supported by Datomic)
- Added new upload-result subcommand to upload migration results to the Wormbase S3 bucket (instead of requiring manual upload)
- Updated release process to use GH personal access tokens
- Security improvements and dependency bumping
0.7.13 (2020-11-23)¶
- Bumped pseudoace dependency version to bugfix migrate-homol DB naming (mismatch between pseudoace and azanium)
- Corrected ws_release_tag git tag availability check
- Changed WB release name parsing strategy, now tag-based rather than FTP-path based (WormBase/db-migration#41)
- Github authorization update (fix WormBase/db-migration#40)
- Fixed release creation vs tagging mismatch (fix WormBase/db-migration#42)
0.7.12 (2020-09-22)¶
- Updated & completed docs
- Bugfixed migrate-homol DB name and DB backup file generation
- Minor logging and code improvements
0.7.11 (2020-07-16)¶
- Updated pseudoace dependency version
0.7.10 (2020-07-09)¶
- Cleanup downloaded artefacts in /tmp
0.7.9 (2020-07-08)¶
- Specify release tag when configuring.
- Source annotated models from a configured github release tag.
0.7.8 (2020-06-23)¶
- Fixed backup-db step for homology migration.
0.7.7 (2020-06-22)¶
- Bump version of pseudoace.
0.7.6 (2020-06-19)¶
- Increase transactor start wait time.
0.7.5 (2020-06-19)¶
- Configure and start transactor before homol migration run.
- Fixed slack notify invocation at end of main migration.
0.7.4 (2020-06-16)¶
- Fixed temp directory cleanup in installers.
0.7.3 (2020-06-16)¶
- Bumped version of pseudoace to 0.7.3 (bring in CLI fix).
0.7.2 (2020-06-15)¶
- Added separate top-level command for running homology migration.
- Bumped version of pseudoace to 0.7.2 to bring in fixes for homology command.
0.7.1 (2020-06-07)¶
- Bring in pseudoace 0.7.1 for import-logs command line bug fix.
0.7.0 (2020-04-06)¶
- Bumped version of pseduoace for CLI homology command fix.
0.60 (2020-03-19)¶
- Bumped version of pseudoace to bring in bug-fix for homology pipeline.
0.59 (2020-03-13)¶
- Fixed issue with datomic_free installer not being re-entrant.
0.58 (2020-03-13)¶
- Ensured error messages are echoed to console during preliminary checks.
0.57 (2020-01-20)¶
- Fixed recording/resetting of current step.
- Fixed click integration for homology import command.
0.56 (2020-01-09)¶
- Fixed command to populate homology db.
0.55 (2020-01-06)¶
- Provide default for db_name when invoking Context.datomic_url.
0.54 (2019-12-03)¶
- Apply retry logic when restarting datomic transactor.
- Bumped version of pseudoace.
- Added two new steps to the migration process (produce homology database).
0.53 (2019-10-08)¶
- Bumped version of pseudoace for bug fixes.
0.52 (2019-09-09)¶
- Pull in new version of pseudoace for bugfix.
0.51 (2019-09-03)¶
- Bumped version of pseudoace to pull in bugfix.
0.50 (2019-09-03)¶
- Bumped version of pseudoace to pull in bugfix.
0.49 (2019-08-30)¶
- Bumped version of pseudoace.
0.48 (2019-08-29)¶
- Fixed locating of pseudoace release archive.
0.47 (2019-07-18)¶
- Modify the way pseudoace is invoked via java jar file.
- Apply any patches from the PATCHES directory on the FTP site.
0.46 (2018-12-11)¶
- Addressed github-reported security vulnerability in package dependencies.
0.45 (2018-12-11)¶
- Bumped versions of datomic and pseudoace.
0.44 (2018-10-24)¶
- Updated to latest version of pseudoace.
- Fixed typo (#35)
- Added missing requriement.
0.43 (2018-06-26)¶
- Configuration of WormBase FTP URL an Slack URL done via configure command.
- Made slack configuration optional, persistent across migration runs.
- Downloading of ACeDB data moved from install step as the first migration step.
- Various bug fixes around the configuration command.
- Updated documentation to match changes to commands.
0.41 (2018-06-19)¶
- Fixed bootstrapping issue.
0.40 (2018-06-19)¶
- The FTP URL is now passed to the azanium configure command, rather than partially parameterised in install commmand(s).
- Fixed bugs with configuration code and logging.
0.39 (2018-06-18)¶
- Removed all AWS specific code, documentation and configuration.
0.38 (2018-06-12)¶
- Fixed dependency issue with awscli.
- Improved docs.
0.37 (2018-06-12)¶
- Updated versions for the next migration run.
0.36 (2018-04-24)¶
- Added admin script for adding new AWS IAM and EC2-host linux user.
- Updated documentation for multi-user migration.
0.35 (2018-04-19)¶
- Use FTP staging area to obtain ACeDB release and class report.
- Improved docs.
0.34 (2018-04-19)¶
- Bumped software versions.
- Updated notification docs.
- Fixed syntax errors.
0.33 (2018-03-06)¶
- Split migration into two stages to speed up the process.
- Fix issue with upgrading package dependencies on install (docs)
- Updated documentation.
0.32 (2018-03-05)¶
- Bumped versions for corresponding versions in pseudoace (WS264 + datomic).
0.31 (2017-12-18)¶
- Release to fix release-script malfunction (!).
0.30 (2017-12-18)¶
- Updated python requirements.
0.29.un-released (2017-12-18)¶
- Bump versions for next migration run.
0.28 (2017-10-30)¶
- Addition of new command “reset-to-step”.
- clean-previous-state command now removes app state file.
- Bump versions for next migration run.
0.27 (2017-09-11)¶
- Source annotated models from release-tag in the Wormbase/wormbase-pipeline repository
- Fixed issue with notifications configuration where configuration could potentially be overridden.
- Bumped versions for next migration run.
0.26 (2017-07-07)¶
- Bumped version of pseudoace.
- Bumped version of datomic-free.
- Bumped release version.
- Removed excise-tmp-data step.
0.25 (2017-05-19)¶
- Bumped version of pseudoace.
- Allow migrate command to work with existing ACeDB database and corresponding pre-gzipped output.
0.24 (2017-04-27)¶
- Bumped data release and pseudoace versions.
0.23 (2017-02-16)¶
- Bumped data release version.
0.22 (2017-02-16)¶
- Bumped versions.
0.21 (2016-11-19)¶
- Bumped versions.
0.20 (2016-11-19)¶
- Download the annotated models file separately (Fixes #8).
- Fix last step (backup and transfer to S3)
0.19 (2016-10-11)¶
- Fixed issue in cleaning up previous migration.
- Allow Datomic URI to be overridden via environment variable.
- Minor fixes to docs.
- Bump data release version to WS256.
- Use the AWS_DEFAULT_PROFILE environment variable rather requiring user to specify with –profile.
0.18 (2016-08-10)¶
- Cleanup data from any previous migration before starting a new one.
- Keep datomic backup directory on disk after S3 upload of tarfile to enable DDB restore.
- Reflect change in pseudoace 0.4.10 (Location of annotated ACeDB models file)
- Fixed issue with wrong path to QA id catalog input path.
- Fixed bucket S3 path for Datomic db backup.
- datomic-free does not support direct s3 upload - work around that with local back and upload via AWS APIs.
- Updates to reflect switch to non-ephemeral instance.
- Bump data version to WS255.
0.17 (2016-06-27)¶
- Minor updates to docs.
0.16 (2016-06-27)¶
- Update install instructions in docs.
0.15 (2016-06-27)¶
- Tweaks to documentation.
0.14 (2016-06-24)¶
- Store application logfile in S3 at the end of each build step.
- Improved docs.
0.13 (2016-06-23)¶
- Updated documentation to match release procedure changes.
0.12 (2016-06-23)¶
- Fix name of entry point zest.releaser uses.
0.11 (2016-06-23)¶
- Fix bug with release hook.
0.10 (2016-06-23)¶
- Fix dependencies.
- Added zest.releaser hook to deploy code/docs to github/github-pages.
- Made the migrate command re-entrant.
0.9 (2016-06-23)¶
- Make this changelog show up in the docs.
0.8 (2016-06-23)¶
- Re-worked documentation to use ghp-import instead of travis-sphinx.
- Add post-release hook to deploy documentation via make-file.
0.7 (2016-06-22)¶
- Pass correct flags to travis-sphinx to get HTML docs built and deployed.
0.6 (2016-06-22)¶
- Fix typo in Sphinx configuration.
0.5 (2016-06-22)¶
- Use Sphinx’s builtin githubpages extension.
0.4 (2016-06-22)¶
- Fixed issue with sphinx build (missing docs/_static)
0.3 (2016-06-22)¶
- Fix docs-build on travis.
0.2 (2016-06-22)¶
- Unified documentation.
- Unified all build steps into a single command azanium migrate.
- Add slack notifications for build progress.
- Prepare automation of documentation build to github pages.
0.1 (2016-06-22)¶
- Initial version.