Changes

LIST OF CHANGES
---------------

release 6.35.0 (2025-01-16)
 - Fix perlbrew installation by installing libdevel-patchperl-perl in
   GitHub runner.
 - Updated ORM classes by ingesting changes for the 'sample' table from the
   production database. Added a class for the 'aliqoute' table.

release 6.34.0 (2024-10-24)
 - Added new delegated methods to WTSI::DNAP::Warehouse::Schema::Result::IseqFlowcell,
   sample_uuid and sample_lims.
 - Updated ORM classes by ingesting changes from the prod database

release 6.33.1 (2024-10-04)
 - Added .github/dependabot.yml file to auto-update GitHub actions
 - GitHub CI - updated deprecated v2 runner action to v3
 - 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 6.33.0 (2024-08-30)
 - Study class updated following the addition of the
   contaminated_human_data_access_group column to the study table.

release 6.32.0 (2024-07-25)
 - add seq_product_irods_locations relationship to IseqProductMetric

release 6.31.1
 - Minor changes to the pac_bio_product_metrics table

release 6.31.0
 - Additional columns added to the iseq_product_metrics table to support
   BGE library metrics reporting.
 - Add columns to pac_bio_product_metrics to store tag level yield
   related metrics and bring other tables up to date

release 6.30.0
 - To help with detecting recent changes, add `last_changed` column
   to PacBio NPG tables and update relevant DBIx classes.
 - Updated DBIx classes from the prod database schema. Two types of changes:
      1. due to a aserver upgrade tp MySQL v.8+
      2. due to database schema changes.

release 6.29.1
 - Switch to Perlbrew to obtain multiple Perl versions

release 6.29.0
 - Add plate_number column to the pac_bio_run_well_metrics table and bring
   DBIx classes up to date.

release 6.28.0
 - Add get_tags methods to pac_bio_run and pac_bio_product_metrics table
   bindings
 - Add 3 columns to the pac_bio_run_well_metrics to store well level
   demultiplexing information.

release 6.27.0
 - Add column to the pac_bio_run_well_metrics to store the ccs dataset
   id for a sample well.

release 6.26.0
 - PacBio metrics tables:
     1. make product id columns not nullable since LangQC relies
        on these ids being available;
     2 set collation for product ids so that it is possible to easily join
       these tables to seq_product_irods_locations table.

release 6.25.0
 - Add columns to the pac_bio_run_well_metrics and pac_bio_product_metrics
   to store QC state for PacBio wells and products
 - Drop redundant index from the pac_bio_product_metrics table
 - Add a new table - gsu_sample_uploads

release 6.24.0
 - Updated the DBIx ORM binding
 - Set up indexes for PacBio tables to support queries from the LangQC
   web application
 - Update action versions in CI

release 6.23.0
 - Add a unique key across pac_bio_product_metrics foreign keys to prevent
   duplication of rows
 - Change CI runner from Ubuntu 18.04 to ubuntu-latest

release 6.22.0
 - Add id_pac_bio_product to pac_bio_product_metrics

release 6.21.0
 - Add run_transfer_complete date to pac_bio_run_well_metrics

release 6.20.1
 - Add new PacBio conf values to pac_bio_run_well_metrics
 - Add substitution metrics from C2A qc check to the iseq_product_metrics
   table

release 6.20.0
 - Add a table for storing one of Illumina's XML files with
   run information, iseq_run_info.
   Add columns to the iseq_run table to capture some values from
   these Illumina files. The choice of the values is driven by the
   current financial reporting need.
   Create a trigger to populate these columns when the record in
   the iseq_run_info is created or updated.
 - Bring DBIx classes up-to-date. 

release 6.19.2
 - additional fields for the pac_bio_run_well_metrics tables and
   bring DBIx classes up-to-date.

release 6.19.1
 - change collation on id_product row of seq_product_irods_locations to
   utf8_unicode_ci to enable JOINs

release 6.19.0
 - bring DBIx classes up-to-date with the prod. database

release 6.18.0
 - bring DBIx classes up-to-date with the prod. database
 - add product_irods table to provide irods paths for data
 - add columns to iseq_external_product_metrics for data deletion status

release 6.17.0
 - Improve record creation for iseq_external_product_metrics.
   Be able to handle complex file names, which explicitly list
   merged lanes, for example, 38421_1-2-4#30.cram. Be able to
   generate correct composition, product id and linking rows for
   such records.

release 6.16.0
 - add user requested control columns to the pac_bio_run_well_metrics
   table
 - Update Copyright statements for all Perl modules according to WSI
   requirements. Retrofit years using dates returned by 'git log' command.
   Example:
     git log -- SOME_MODULE.pm | grep 'Date:' | cut -d ':' -f 4 | \
     cut -d ' ' -f 2 | uniq | sort -g | xargs echo | \
     perl -nle '$_=~s/\ /,/g; print "Copyright (C) $_ Genome Research Ltd."'
 - DBIx classes updated and new classes added by running scripts/make_schema.pl
   against the production database. cherrypicked_sample view is excluded from
   the database inspection, DBIx does not like the definition. 
 - Add additional columns to the iseq_heron_product_metrics table to capture
   the pipeline's URL, ivar_md minimum depth value used with ivar and metrics
   for the consensus computed with an alternative ivar minimum depth ivar_amd.

release 6.15.0
 - Move from Travis CI to GitHub Actions.
 - If a WHERE clause in a SELECT query for the iseq_flowcell table
   specifies id_flowcell_lims, the query runs faster if the value
   is supplied as a string rather than an integer. If the value is
   supplied as an integer, the query cannot use the search index,
   resulting in a full table scan, during which the values in the
   id_flowcell_lims column are converted to doubles. Some of the
   values in the column are true strings which cannot be converted
   to doubles. Thousands of such values give thousands of warnings.
   To make queries more efficient, the id_flowcell_lims value
   in the WHERE part of the DBIx query is explicitly converted to
   strings. Clear difference can be seen when running the code
   with DBI_TRACE enabled.

release 6.14.0
 - add iseq_run table to enable
     a direct join between the iseq_flowcell ad iseq_run_status tables;
     to provide information about the run folder name
 - add hifi related columns to pac_bio_run_well_metrics table

release 6.13.0
 - add tables pac_bio_run_well_metrics and pac_bio_product_metrics 
   to store metrics extracted from PacBio's SMRT Link LIMS

release 6.12.0
 - a new iseq_product_ampliconstats table to store per sample
   per amplicon statistics that is generated by 'samtools
   ampliconstats'

release 6.11.0
 - iseq_heron_product_metrics table:
     set index on the id_run column,
     add pp_name and pp_version columns to capture info
     about the pipeline, which generated the data

release 6.10.0
 - add id_run column to the iseq_heron_product_metrics table
 - to allow for deletion of iseq_product_metrica rows, drop
   the foreign key constraint on the id_iseq_product column in
   the iseq_heron_product_metrics table, keep the relation
   definition in the DBIx class
 - update the DBIx class for the cgap_heron table
 
release 6.9.0
 - ml warehouse LIMS drivers - define additional delegated
   to sample objects methods 
 - DBIx class for a new iseq_heron_product_metrics table
 - DBIx classes updates for latest changes in ml warehouse database
 
release 6.8.0
 - capture latest changes/additions in ml warehouse database

release 6.7.0
 - PSD added  pac_bio_run_name field to pac_bio_run table to support
   runs being created in traction as well as SequenceScape LIMs
 - iseq_product_metrics table - a new column to store the outcome
   of product uqc
 - iseq_external_product_metrics - a new column to store product
   destination
 - iseq_run_lane_metrics table - added columns to store per-lane
   Illumina InterOp data

release 6.6.0
 - add instrument_external_name column to the iseq_run_lane_metrics
   table

release 6.5.0
 - more detailed comments for some columns.
 - 'annotation' column reduced to 15 chars since it's not free text
 - added columns for whole genome yield and end of phase2 analysis
   date
 - fixed spelling in one of the columns, ie changed column name
   from archive_conformation_date to archive_confirmation_date

release 6.4.0
 - iseq_external_product_component table redesign to allow for
   rows on iseq_product_metrics table to be deleted and recreated
   without making data in the linking table invalid
 - yield column in the iseq_external_product_component table changed
   from integer to float to correctly accommodate source data
 - code to creating rows in the iseq_external_product_component table,
   which will be run on row creation the and sometimes on row update
   for rows of the iseq_external_product_metrics table; this code will
   also be used to create a backlog of linking rows for existing
   iseq_external_product_metrics table rows

release 6.3.0
 - table update for iseq_external_product_metrics:
   drops id_iseq_pr_metrics_tmp and a foreign key based on it
     since maintenence will be difficult,
   adds index on id_iseq_product to enable using this column
     in joining to iseq_product_metrics table on a similar column,
   adds an indexed id_run column in case stats by run is needed
 - insert and update DBIx IseqExternalProductMetric class
   customisation to ensure that composition data and id_run
   columns are filled in

release 6.2.1
 - nrd_assessment column comment update: include 'NA' as a valid value

release 6.2
 - update definition of iseq_external_product_metric table
   - fastqc columns become varchars
   - rename column qc to qc_overall_assessment
   - new column qc_status
 - update DBIx classes to match new table definition

release 6.1
 - update DBIx classes from prod database
 - update definition of iseq_external_product_metric table

release 6.0
 - add new tables for externally processed data

releaes 5.1
 - allow to store longer composition JSON strings in the iseq_product_metrics
   table

release 5.0
 - added target autosome fields to iseq_product_metrics
 - added DBIx binding for the bmap_flowcell table for the
   BioNano Saphyr instrument

release 4.0
 - iseq_product_metrics table: make id_iseq_product column not nullable,
     set unique constraint on it
 - a new table iseq_product_components - linking table for product records
     in iseq_product_metrics

release 3.1
 - add column 'nrd_percent' for non-reference discordance to the
    'iseq_product_metrics' table

release 3.0
 - 'last_changed' columns added to both 'iseq_product_metrics' and
   'iseq_run_lane_metrics' tables
 - 'workflow_type' and 'instrument_side' columns added to the
   'iseq_run_lane_metrics' table
 - 'qc_seq' column addedto the 'iseq_run_lane_metrics' table
 - redundant 'iseq_pm_run_index' indexed dropped from 'iseq_product_metrics'
   table
 - changes to enable saving results for merged entities to'iseq_product_metrics':
     NOT NULL constraint dropped from 'id_run' and 'position' columns;
     nullable 'id_iseq_product' column added to save composition digest;
     nullable 'iseq_composition_tmp' added to save a short form of composition
     JSON, needed because we do not have the linking table yet

release 2.11
 - added metric column to iseq_product_metrics for RNA: MT expression in pct of TPM.
 - add target fields to iseq_product_metrics

release 2.10
 - added metrics columns to iseq_product_metrics for GbS

release 2.9
 - added metrics columns to iseq_product_metrics (for RNA)
 - superfluous database indexes dropped
 - DBIx schema update for primer_panel
 - added columns tag_hops_percent and tag_hops_power to iseq_run_lane_metrics table

release 2.8
 - added DBIx binding for oseq_flowcell table (describes LIMS info for ONT)
 - Travis build - for Perl v 5.22 change to interpreter with threaded support

release 2.7
 - DBIx binding update

release 2.6
 - ensure lists of study users email addresses do not contain empty or undefined entries

release 2.5
 - add column run_priority to iseq_run_lane_metrics table

release 2.4
 - change in use of cycles value; expected_cycles calculated from iseq_flowcell read lengths and length of tag sequence(s).

release 2.3
 - library_type added to LibraryDigest entity

release 2.2
 - DBIx schema update

release 2.1
 - small change to LibraryDigest to support non SS tracked libraries.
 - use custom build base class to get correct version in a distribution
 - Travis tweaks
   + add deployment to GitHub Releases
   + add newer 5.22 Perl to travis build matrix and allow container builds (sudo false)

release 2.0
 - update to test script and data for filters in LibraryDigest
 - added DBIx class for the new pacbio LIMs data table

release 1.8
 - parameterized WTSI::DNAP::Warehouse::Schema::Query::IseqFlowcell role
   to allow for query on run id
 - iseq_product_metrics table: add columns to store in-house qc values

release 1.7
 - extend field size for mean_bait_coverage RT#495558, Change request No6

release 1.6
 - change the comment on iseq_run_lane_metrics.unexpected_tags_percent
 - update DBIx schema to reflect this change and propagate any changes
   to other tables of the live database

release 1.5
 - Ability to query by id_study_lims in LibraryDigest
 - Added unexpected tag and chimeric fields to iseq_product_metric and iseq_run_lane_metric tables
 - Ability to restrict by (legacy) library id
 - Added extra fields to entity which are needed by library merging script for adding to iRODS meta data.
   Key changed to included cycle count as well as paired_flag. Corresponding test updated. 

release 1.4
 - update DBIx binding to include second index sequence
 - check that flowcell LIMs id and barcode map 1:1 (RT#481156)

release 1.3
 - mapping for additional lims interface fields for sample data

release 1.2
 - value of the GCLP data lims flag has changed - reflect this

release 1.1
 - bug fix in readonly variable declaration

release 1.0
 - DBIx schema update following database schema changes
 - contains_human_dna and contaminated_human_dna columns have been converted
   from varchar to tinyint, inflators/deflators for these columns dropped

release 0.7
 - new module - library digest - retrieves information about libraries,
     groups it either by library or by sample

release 0.6
 - added a role providing methods to determine what LIMs system the record originated from

release 0.5
 - ensure contains_human_dna and contaminated_human_dna behave in a boolean manner
 - update mapping of library_id lims field to database fields
 - ensure missing study link does not lead to code failure when accessing e-mails of followers, etc.
 - add mapping for lane_id

release 0.4
 - following db schema changes, update the DBIx binding

release 0.3
 - added WTSI::DNAP::Warehouse::Schema::Query::IseqFlowcell - a role for querying
   the flowcell table knowing one of flowcell identifies
 - DBIx object for flowcell row: fields neccessary for NPG lims interface
   added

release 0.2
 - foreign key into the flowcell table dropped from the run lane metrics table
 - a few autoqc results columns dropped from the run lane metrics table
 - extra column for verify_bam_id results added to the product metrics table
 - columns for modality of the insert size results added to the product metrics table

release 0.1
 - initial release