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CHANGELOG.md

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Change-log

[0.7.8] - (2020-11-03)

  • Use provided URL as homology DB datomic URI in homol-import
  • Minor README and code cleanup and improvements
  • Minor deps.edn and pom.xml cleanup

[0.7.7] - (2020-07-16)

  • Attempt to delete databases before creating

[0.7.6] - (2020-06-22)

  • CLI error handling fix.

[0.7.5] - (2020-06-19)

  • CLI error handling fix.

[0.7.3] - (2020-06-16)

  • Bugfix for CLI function.

[0.7.2] - (2020-06-15)

  • Homology import: fixes and refactoring.

[0.7.1] - (2020-04-06)

  • Added option to reset log directory (recursively remove all contents).

[0.7.0] - (2020-03-19)

  • Fixed misplaced parenthesis.

[0.6.9] - (2020-01-20)

  • Homology pipeline fixes.

[0.6.8] - (2020-01-20)

  • Fixed pipeline for homology database creation.

[0.6.7] - (2019-10-08)

  • Fixed breaking WS273 import due to work done feature/patching.
  • Added homology import support (separate database).

[0.6.6] - (2019-09-08)

  • Fixed bug with printing path in import-logs phase.

[0.6.5] - (2019-09-03)

  • Fixed bug with refactoring done for ACe patching.

[0.6.4] - (2019-09-03)

  • Fixed bug with log fix-ups.

[0.6.3] - (2019-08-30)

  • Fixed missing paramter in function call.

[0.6.2] - (2019-07-18)

  • Another redeploy due to issues with mvn deploy.

[0.6.1] - (2019-07-18)

  • Redeploy of 0.6.0 due to script error.

[0.6.0] - (2019-07-18)

  • Used clojure dev tools (clj)
  • Removed AOT compilation
  • Used leiningen 2.9.1+
  • Used seancorfield/depstar for building uberjar
  • Changed how the CLI program is invoked (dev and prod, see README)
  • Added command line program to generate EDN patches from ACe input(s).
  • Implemented CLI for patching the database.

[0.5.9] - (2018-12-11)

  • Bumped version of datomic to 0.9.5703
  • Added generated schema for WS269.

[0.5.8] - (2018-10-24)

  • Added generated schema for WS267.

[0.5.7] - (2018-04-19)

  • Bumped version of datomic to 0.9.5697.
  • Added generated schema for WS265.

[0.5.6] - (2018-03-05)

  • Bumped version of datomic (pro + free) 0.9.5656
  • Updated clj-time to latest version.
  • Addeed generated schema for WS264.

[0.5.5] - (2017-12-18)

  • Bumped versions of datomic-pro and datomic-free to 0.9.5651.

[0.5.4] - (2017-10-30)

  • Updated version of datomic-free to match datomic-pro.

[0.5.3] - (2017-10-30)

  • Upgrade to datomic-pro version 0.9.5561.56
  • Fixes issue with QA report parsing.

[0.5.2] - (2017-07-07)

  • Bumped various dependency versions, notably datomic-pro to version 0.5561.50.

[0.5.1] - (2017-05-19)

  • QA report now uses new ACeDB id catalog csv format.

[0.5.0] - (2017-04-27)

  • Added distinct-by utility function.
  • excise-tmp-data CLI command now correctly requests and syncs index before invoking gc-storage.

[0.4.15] - (2017-02-16)

  • Added gene rated schema for WS257.
  • Make output of generated schema valid EDN.
  • Use latest version of datomic 0.9.5554.
  • Added API for getting the name of the main datomic database.
  • Added API for getting the version of package.

[0.4.14] - (2016-11-11)

  • Allow migrations with no locatable schema and/or schema fixups.

[0.4.13] - (2016-11-09)

  • Bugfix release for 0.4.12

[0.4.12] - (2016-11-09) (DO NOT USE)

  • Support suppression of schema "fix-ups" (for smallace/training databases).

[0.4.11] - (2016-10-10)

  • Add generated schema for WS256
  • Ability to specify max-count and max-text for log partitioning via a command line option to the import-logs command.
  • Use composite lein profiles.

[0.4.10] - (2016-07-22)

  • Bump version of various packages, notably datomic-pro and dynamodb aws-sdk libraries.
  • Explicitly pass the annotated models filename as arguments to the CLI (Annotated ACeDB models file now lives in the wormbase-pipeline repository).

[0.4.9] - (2016-07-07)

  • When dumping .ace files, only present the leaf tag (as the tace Show command) - enables easier comparisons of ace output.
  • Add functions for dumping a query to .ace files

[0.4.8] - (2016-06-24)

  • Fix wrong exit-code when helper.gz is encountered in sort-edn-log.sh.

[0.4.7] - (2016-06-20)

  • 2_point_data ACeDB class renamed to two-point-data in annotated models (#33).
  • Fix for circular xrefs for phenotype and phenotype_not_observed in annotated models (#46)
  • Bug in sort-edn-log.sh - Sort command now uses the temporary sort directory.

[0.4.6] - (2016-06-15)

  • Added back missing xbin function in pseudoace.binning.

[0.4.5] - (2016-06-14)

  • Remove hard-dependency on datomic-pro. Library users will now have to choose which flavour (and version) of datomic to include.
  • Made all functions in the pseudoace.binning module public.
  • EDN log sorting script now allows parallel execution.
  • Annotated models for WS255 (including generated EDN schema)

[0.4.4] - (2016-05-12)

  • Support distributing a release bundle using either datomic-free or datomic-pro.
  • Add generated schema for WS253, WS254
  • Various minor fixes for the command line interface.

[0.4.3] - (2016-04-28)

  • Rollback version of aws library.

[0.4.2] - (2016-04-28)

  • Updated documentation.

[0.4.1] - (2016-04-28)

  • Use lein release for releases.
  • Bump versions of datomic and storage dependencies.

[0.4] - (2016-04-25)

  • Moved sorting of logs files back out to the shell.
  • Fixed lingering namespace issues in pseudoace.acedump.
  • Use datomic.api.tempid in code, not reader-literals.
  • Use the script scripts/bundle-release.sh to create a bundle for deploying to servers and running the importer.
  • Updated README (development and release instructions).
  • Added development tools to "dev" profile in leiningen project configuration.
  • Enable multiple storage profiles in lein project.
  • Added script to generate release bundle.
  • Models file is now defaults to models/models.wrm.annot (no need to pass on command line to sub-commands)
  • Unified the various additional schemata into a single module.
  • Import will no longer attempt to transact EDN logs older than the latest transaction date.
  • Report now generates two files per class when non-zero missing and added counts are encountered for easy diffing of object names.

[0.3.1]

  • Added ability to generate a report for comparing a dump of classes to values against those stored in the database.

[0.3.0]

  • Fix error with old-namespace: acetyl is no longer used, and has been in-lined into the pseudoace package.

[0.2.0]

  • Re-organised project structure.
  • Separation of components into separate repositories.
  • Added basic unit test structure.
  • Removed dependency on perl for sorting EDN files.
  • Fixed minor issues with command line interface.

[0.1.0]

  • Initial version