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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

1.0.0 2022-03-07

Changed

  • In honour of its valuable service and strong track record of 22.8 million API requests, Ocarina is now awarded the honorary version of 1.0.0

0.49.0 2022-02-09

Changed

  • Added published_date column to end of get pag --mode pagfiles output

Fixed

  • Limited columns output by get pag --mode pagfiles to prevent new columns breaking older versions of Ocarina

0.48.0 2022-02-06

Changed

  • Configuration is now handled with Ffurf, tidying up ocarina.util.get_config as well as offering more flexibility
  • --print-config will additionally print a status line to clearly communicate whether the loaded configuration is valid
  • --print-config will load and print an invalid configuration for inspection before exiting non-zero, rather than exiting non-zero without displaying anything
  • --print-config will use rich to print a nice table of the configuration if --boring is not specified

Added

  • OCARINA_CONF_FILE environment variable can now be used to change the default ~/.ocarina configuration location
  • Top level --profile <profile> parameter can now be used to select which configuration to load from a corresponding profile.<profile> object in Ocarina configuration JSON

0.47.3 2022-01-25

Changed

  • get pag --mode pagfiles now supports prepending a header with --output-header and will translate suppression status to "SUPPRESSED" or "VALID" rather than printing a bool

0.47.2 2022-01-10

Changed

  • .ocarina file automatically created if it does not exist instead of suggesting the user creates it themselves
  • Configuration and token files are created with better default permissions by setting umask
  • Emits a warning if non-user read or write permissions are detected on the Ocarina configuration or token cache

0.47.1 2021-12-08

Changed

  • empty biosample command now supports --metadata when uploading single empty biosamples
    • Note that using --metadata with --ids is not supported and will emit a client side warning
  • api.put_force_linked_biosample supports optional metadata parameter

Fixed

  • Corrected wrong version number in last CHANGELOG entry (46.1 was labelled as 46.0)

0.46.1 2021-12-02

Changed

  • get pag supports --published-before

0.46.0 2021-10-15

Added

  • New experimental (unsupported) functions added to importable API client
    • put_force_linked_biosample
    • put_library
    • put_sequencing
  • --print-config option will dump out the Ocarina configuration (including secrets) for inspection

Changed

  • MAJORA_TOKENS_FILE config option (supported both by --env and ~/.ocarina JSON) allows the tokens cache to be placed in a user-determined location (otherwise defaults to existing ~/.ocarina-tokens)

Fixed

  • library_primers and library_protocol are now correctly sent to Majora when using the singular --biosample option for put library

0.44.2 2021-10-15

Added

  • oauth authorise will authorise an OAuth token for a particular endpoint for later use

Changed

  • empty subcommand supports --sudo-as command line option

0.44.0 2021-08-14

Changed

  • Util function _wait_for_task now controls all task result fetching for commands to remove significant code duplication
  • get sequencing and get sequencing --faster have a configuration stanza to correctly support OAuth with majora2.view_biosampleartifact scope
  • api.majora.task.get has a configuration stanza to correctly support scopeless OAuth
  • get pag, get dataview and get sequencing will correctly support using --task-id (with or without --task-wait) to pick up a wait loop that was interrupted without issuing another task request
  • Improved sysexit error codes for task waiting failure modes

0.43.0 2021-08-11

Changed

  • pag suppress has a configuration stanza to correctly support OAuth with can_suppress_pags_via_api scope
  • get summary and get outbound-summary have configuration stanzas to correctly support scopeless OAuth

0.42.1 2021-08-10

Changed

  • Changed exit codes to cover more cases using codes recommended by sysexits

Fixed

  • Error message and exit code returned in the case where the .ocarina or .ocarina-tokens JSON is malformed

0.41.4 2021-07-30

Fixed

  • Ocarina will reload OAuth2 tokens from disk before each request to reduce the likelihood of polling queries from failing

Changed

  • get pag has a configuration stanza to correctly support OAuth with temp_can_read_pags_via_api scope

0.41.2 2021-06-11

Changed

  • get biosample subcommand now supports OAuth using majora2.view_biosampleartifact scope

0.41.1 2021-06-05

Added

  • Spruced up ocarina info using the very fancy rich library, you can disable this with --boring

0.40.2 2021-05-25

Changed

  • ocarina empty biosample now has two modes:
    • Existing --ids hoot meow honk mode allows one or more biosample artifacts named central_sample_id to be forced into existence, unchanged for backward compatability
    • --central-sample-id hoot --sender-sample-id secret_hoot allows one biosample named central_sample_id with its sender_sample_id to be forced into existence

0.39.2 2021-05-24

Changed

  • get dataview --output-table now handles dataviews with nested data, one level deeper

Fixed

  • Fixed incorrectly documented version number for last release in CHANGELOG, incorrectly referred to as 0.31.1 instead of 0.39.1

0.39.1 2021-05-23

Added

  • OCARINA_QUIET config option (supported both by --env and ~/.ocarina JSON) can be set to non-zero (0) to suppress all non-output messages without --quiet
  • --no-banner command line option suppresses the welcoming ocarina banner
  • OCARINA_NO_BANNER config option (supported both by --env and ~/.ocarina JSON) can be set to non-zero (0) to suppress the welcoming ocarina banner without --no-banner
    • You're welcome, @m-bull [#12]

Changed

  • ocarina info metadata lines are now printed in key sorted order

0.39.0 2021-04-27

Added

  • Experimental info command to grab basic metadata on any artifact in Majora

0.38.4 2021-04-26

Changed

  • put tag subcommand now supports OAuth using majora2.add_majorametarecord majora2.change_majorametarecord scopes

0.38.3 2021-04-22

Added

  • Better late than never, CHANGELOG.md will now document notable changes to Ocarina

Changed

  • get biosample-validity subcommand now supports OAuth using majora2.view_biosampleartifact scope