Changes

Unreleased 

Release 3.25.0 (2024-10-25)

 - Added csi index file type to WTSI::NPG::iRODS::Annotator
  
Release 3.24.1 (2024-10-04)

 - Fix handling of undefined data release strategy
 - Improve error handling when listing collections (add early returns).
 - Move Perlbrew install to a script so that it can be used by both
   GitHub Actions and Docker.
 - Added .github/dependabot.yml file to auto-update GitHub actions
 - Following a release on 07/09/2024, see https://metacpan.org/dist/App-perlbrew/changes
   the checksum of the script served by https://install.perlbrew.pl had changed.
   https://install.perlbrew.pl is a redirect to raw
   https://github.com/gugod/App-perlbrew/blob/master/perlbrew-install, so
   the change originates from GitHub and can be trusted. Our CI flow compares
   the checksum of the downloaded script to the expected value. We now store
   an updated expected checksum value, which corresponds to the latest release.

Release 3.24.0 (2024-09-02)

 - populate_wtsi_irods_groups now sets ss_<STUDY_ID>_human group membership if
   these have been set in the contaminated_human_data_access_group field

 - Change populate_wtsi_irods_groups.pl to only populate iRODS
   study access groups with all seq iRODS users for SS studies
   with empty data access where the study is not managed e.g.
   submitted to EGA not ENA

Release 3.23.0 (2024-07-25)

 - Add PACBIO_ISOSEQ_PRIMERS to Metadata - required for archiving
   analysis output from IsoSeq analysis jobs
 - Add fastq and gff as a standard ancillary file type

Release 3.22.2 (2024-05-24)

 - Add iRODS 4.3.2, remove 4.3-nightly

Release 3.22.1

 - avoid uninitialized value in addition when human group not created

Release 3.22.0

 - Introduced ss_<STUDY_ID>_human iRODS group to provide limited
   access to split-out human data. Specific changes:
     - exposed ensure_group_exists method from iRODS::GroupAdmin
     - populate_wtsi_irods_groups creates _human iRODS groups
     - tests fixtures extended to include these new iRODS groups
     - reimplemented expected_groups from WTSI::NPG::irods::Path
       to return all groups that are appropriate for an object or
       a collection; this method consolidates all logic about
       study-related access to data, this logic was previously split
       between WTSI::NPG::irods::Path and WTSI::NPG::irods::DataObject
 - Fixed incorrect example in POD

Release 3.21.0

 - Add iRODS 4.3.1 Ubuntu 22.04 as a required test target
 - Handle optional rodsadmin group
 - Update test matrix iRODS versions
     Remove the combination of 4.2.11 clients with a 4.2.7 server
     Add the combination of 4.2.7 clients with a 4.2.7 server
     Add the combination of 4.3-nightly clients with a 4.3-nightly server
 - GHA: move irods client deployment and singularity cache to HOME
   instead of workspace/ repo checkout dir.
 - Add Perl 5.34 to CI matrix

Release 3.20.0
 - Add iquest wrapper

Release 3.19.0
 - Add PACBIO_PLATE_NUMBER to Metadata - required for
   multi plate Revio runs

Release 3.18.5
 - Fix failure due to a fragile test

Release 3.18.4
 - Add Singularity container support for iRODS clients

Release 3.18.3
 - Use github hosted images for ci

Release 3.18.2
 - Update version of github actions
 - Update iRODS permissions policy documentation

Release 3.18.1
 - Change CI runner from Ubuntu 18.04 to ubuntu-latest

Release 3.18.0

 - Update baton version in github actions workflow to 4.0.0
 - baton version required >= 2.1.0 < 5

Release 3.17.1

 - Update baton version in github actions workflow to 3.3.0
 - Remove iRODS 4.2.10 from github actions workflow

Release 3.17.0

 - Add SamHaplotag files
 - Remove -T option from icommands execution
 - Add iRODS 4.2.11 to github actions workflow
 - Bug fix: Correctly resolve local paths in get_object

Release 3.16.0

 - Add data object size and verify checksum support

Release 3.15.1

 - Improve variable names and comments in iRODS test setup.

Release 3.15.0

 - Add iRODS 4.2.10 to the test matrix
 - Remove remove_replicate and prune_replicates methods
 - Bugfix: Typo in copy_collection method

Release 3.14.0

 - Move from Travis CI to GitHub Actions.
 - add copy and move colleciton utilities
 - baton version required >= 2.1.0 < 4

Release 3.13.0

 - Add baton 2.1.0 to the test matrix
 - Switch from List::AllUtils to List::MoreUtils implementation of 'zip' because
   of a breaking API change in the former.     

Release 3.12.0

 - Order Conda channels for tests so that NPG channels have highest priority
   and conda-forge the lowest.
 - Remove RabbitMQ code
 - Rename GBS_PLEX_NAME = gbs_plex to primer_panel in Metadata 
   to match field in mlwarehouse.
 - Due to a bug in iRODS 4.2.7, the imv command doesn't work cleanly for
   collections. This is especially evident on federated zones. Added
   move_collection workaround to mitigate this problem.

Release 3.11.0

 - Bugfix: handle re-uploading files with no checksum stored
   in iRODS
 - Bugfix: correct the iRODS 4.2.8 test matrix configuration

Release 3.10.0

 - Bugfix: handle listing non-existent collections cleanly.
   See https://github.com/wtsi-npg/perl-irods-wrap/issues/208

 - Remove from test matrix iRODS 4.1.12
 - Add iRODS 4.2.8 to test matrix
    
   iRODS 4.2.8 is marked as an expected failure because we have not yet
   built a Conda package of irods-icommands 4.2.8

 - Remove support for iRODS 3.x

Release 3.9.1
 - Bugfix: stop IPC::Run process pump before exiting

Release 3.9.0
 - Update tests to use iRODS 4.2.7 clients with 4.2.7 server
 - Fix data object replacement checksum behaviour in line with test

Release 3.8.0
 - Drop iRODS 3 support, add 4.2 support (ienv parsing)
 
Release 3.7.0
 - Requires baton >= 2.0.1
 - Added bqsr_table and tbi to recognised file types.

Release 3.6.0
 - Added PACBIO_DATA_LEVEL metadata for PacBio - data_level denotes whether 
   the sequence data is primary; off instrument base calls -or- secondary; has 
   been subsequently post processed via additional analysis e.g. raw subreads 
   from the same SMRTbell sequence have been combined to produce a one 
   high quality (circular consensus) sequence.

Release 3.5.1
 - Fixed null dereference in Collection::collection_checksums

Release 3.5.0
 - Added a new metadata attribute - id_product - to capture the digest
   of composition JSON

Release 3.4.0
 - Allow publishing from read-only directories
 - Reduced the log level of creating missing MD5 cache files from
   warning to debug

Release 3.3.0
 - Add composition to metadata
 - Added COMPONENT to standard metadata
 - Add bcfstats as a standard file type
 - Add the public group members to sequencing studies on ONT platforms

Release 3.2.0
 - Added hts genotype suffixes to Annotator
 - Switched to disposable-irods 1.3 (uses WSI S3 for iRODS packages).
 - Added gbs_plex to Metadata.pm and hts genotype to non_compress_suffixes
   in Annotator

Release 3.1.0
 - Added "hops" to HTS ancillary suffixes list

Release 3.0.2
 - Support for single-server mode
 - Added "quant" and "tab" to HTS ancillary suffixes list

Release 3.0.1
 - Support for baton versions >=1.0.0 and <=1.1.0

Release 3.0.0
 - API change for WTSI::NPG::iRODS::Publisher
   - Publication returns iRODS DataObject or Collection, instead of string
   - Affects methods: publish, publish_file, publish_directory
 - Remove the list_path_details method from WTSI::NPG::iRODS
 - RabbitMQ:
   - Messaging for method calls in Publisher as well as iRODS
   - Reportable Role refactored into Base, PublisherMQ, and iRODSMQ Roles
   - Enable RabbitMQ for Travis tests
   - Bugfix; no error if RabbitMQ tests are disabled and
     Net::AMQP::RabbitMQ is not installed 

Release 2.8.2
 - Make internal iRODS.pm method calls private
 - RabbitMQ: add UUID to message header; change routing key format
             use API for baton calls

Release 2.8.1
 - Disabled staging/unstaging data objects to work around a baton bug
   in the function to move/rename objects. This also removes the
   complexity of staging and unstaging data objects which provided
   little benefit in practice.

Release 2.8.0
 - (Un)staging new data objects
      error results in deletion rather than tagging for inspection
      post-failure "staging=1" AVU ignored rather than error
 - New PacBio legacy metadata
 - Switch to baton-do as the single baton client
 - Support for RabbitMQ messaging to report method calls
 - Stop using imv, ichksum and md5sum executables
 - Add fasta type
 - Use baton version 1.0.0 

Release 2.7.1

 - Bug fix and speed-up for populate_wtsi_irods_groups.pl 

Release 2.7.0

 - Bugfix; clean up any iRODS groups created by the test suite
 - Added methods describing know filename suffixes
 - Added metadata for BioNano
 - Added metadata for 10X
 - Added metadata for PacBio pbi files

Release 2.6.1

 - Use ml_warehouse
 - Added metadata for PacBio
 - Fix for staging iput where the target path is a collection 
 - check for cases where a user's gidNumber doesn't have a group
 - Travis CI: build package under perl v.5.22
 - Improved handling of file suffix metadata
 - Support baton versions  >=0.16.4 and <=0.17.1

Release 2.6.0

 - Bugfix; correctly report multiple AVUs found for a given attribute
   by get_avu in logs.

 - Support baton versiosn  >=0.16.4 and <=0.17.0

 - Backported the basic data object Publisher (and support classes) from
   npg_irods.

 - Switched test matrix from iRODS 4.1.8 to iRODS 4.1.9

Release 2.5.0

 - Switch to logging on a per-class basis.

 - Ensure test dependencies are installed.

Release 2.4.0

 - Added a method parameter to allow server-side checksum calculation
   to be deferred when adding or replacing data objects.

 - Muffled spurious errors from baton-list (requires baton 0.16.4).

 - Added iRODS 4.1.8 to the test matrix.

 - In testing, the default resource is now 'testResc'.

Release 2.3.0

 - Added support for data object replicate management.

 - Added support for use#zone syntax in permissions,

 - Requires baton 0.16.3 to support use#zone syntax.


Release 2.2.0

 - Added caching of iRODS paths for performance.

 - Added caching of object AVUs for performance.

 - Added caching of object AVUs for performance.

 - Added a new dependency on Cache::LRU

Release 2.1.0

 - Added reference_name and gene expression metadata keys.

 - Added destructor to WTSI::NPG::iRODS responsible for stopping
   child processes.

 - Changed dcterms metadata values to use the normal :: namespace
   delimiter, instead of underscore (e.g. dcterms_title to
   dcterms::title). These have not yet been used in production.

 - Added metadata keys alt_process, alt_target, alignment_filter.

 - Added caching behaviour for data access groups to avoid executing
   igroupadmin in WTSI::NPG::iRODS.

 - Removed the TODO flag on UTF-8 round tripping.

 - Added dependency on MooseX::StrictConstructor.

Release 2.0.3

 - Set the TODO flag on UTF-8 round tripping as a workaround for some
   iRODS instances.

 - Set tests to fail rather than skip if they exit early.

 - Use cpanm to install dependencies on Travis CI.

 - Added alignment_filter and alt_target sequencing metadata keys.

Release 2.0.2

 - Added support for a TEST_PERFORMANCE environment variable. If set,
   the performance tests will be run. The default is not to run them.

 - Added support for the TEST_AUTHOR environment variable. If set and
   the iRODS test environment is not declared, the tests will fail. If
   not set and the iRODS test environment is not declared, the tests
   will skip.

 - Tests now require explict declaration of the iRODS test environment.

Release 2.0.1

 - Requires baton 0.16.0 or 0.16.1

Release 2.0.0

 - New methods WTSI::NPG::iRODS::replicates. New attribute
   WTSI::NPG::iRODS::DataObject::replicates. New class
   WTSI::NPG::iRODS::Replicate.

 - Requires baton 0.16.0

 - New method WTSI::NPG::iRODS::match_baton_version to permit version
   ranges of compatible baton installations to be specified.

 - New methods WTSI::NPG::iRODS::make_avu, WTSI::NPG::iRODS::sort_avus and
   WTSI::NPG::iRODS::remove_duplicate_avus.

 - New package WTSI::NPG::iRODS::Metadata which exports values to describe
   metadata. Removed Moose roles WTSI::NPG::iRODS::Annotation and
   WTSI::NPG::Annotatable.

 - Support both $WTSI::NPG::iRODS::Metadata::SAMPLE_CONSENT and
   $WTSI::NPG::iRODS::Metadata::SAMPLE_CONSENT_WITHDRAWN in updating
   ACLs from study metadata.

Release 1.8.0

 - New methods WTSI::NPG::iRODS::is_collection and
   WTSI::NPG::iRODS::is_object.

 - New attribute WTSI::NPG::iRODS::group_filter.

 - Checking of string arguments representing iRODS paths is now
   tighter where they are expected specifically to be a collection or
   data object.

 - Metadata values are now able to be set to '0' (bug fix).