From ad5bbf0cadd8aaafe6b1d1cb0b3270ad1e7659f0 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 31 Oct 2023 10:05:46 +0000 Subject: [PATCH 1/2] Record all recent changes --- Changes | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/Changes b/Changes index be449358..f3ef1b9e 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,35 @@ LIST OF CHANGES + - Removed the use of 'xml' lims driver from all tests. + - Deleted 'xml' lims driver class and all classes, which supported this + functionality, together with all related tests and test data. + - In release 97.0.0, ihe default LIMS driver type in samplesheet generation + was changed to 'ml_warehouse'. Following this change, the code for + auto-generation of MiSeq default samplesheets is now simplified to exclude + an explicit creation of LIMS objects. + - Changes to st::api::lims, which are not related to the 'xml' lims driver + removal: + - deleted all previously deprecated methods ('seq_qc_state', + 'associated_lims', 'associated_child_lims', 'associated_child_lims_ia'); + - deleted methods, for which we do not have data in ml warehouse, our + primary source of LIMS data ('request_id', 'project_id', 'project_name'); + - deleted all code for computing inline tag indexes and inferring + tag sequences and library types from sample description since + definitions like this have not been in use for the last six years; + - reimplemented the 'reference_genome' method to exclude a fallback to + a study reference for tag zero and lane-level objects when samples + have different references. + - Restricted the 'all_lanes_mergeable' flag in the 'lonf_info' role to + NovaSeq Standard workflow, ie dropped an additional case of HiSeq Rapid Run + since HiSeq instruments are no longer used. + - Updated DBIx classes from the prod database. Changes are due to the MySQL + database server upgrade to v8.+ + - Finding the runfolder path - stopped errors being raised when a runfolder + is found in 'analysis' or 'outgoing' in the presence of a duplicate runfolder + in 'incoming' (the duplicates in 'incoming' are sometimes created by + instruments well after the run was mirrored and the runfolder moved to + 'analysis'). The duplicate runfolder in 'incoming' is disregarded'. + release 97.0.0 - Change CI workflow to standard file name - Change to Perl versions from Perlbrew From 10352367d73b68154838e17f2579858ed9148a41 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 31 Oct 2023 18:01:21 +0000 Subject: [PATCH 2/2] Fixed typos and deleted superfluous commas --- Changes | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Changes b/Changes index f3ef1b9e..8f538bfc 100644 --- a/Changes +++ b/Changes @@ -1,9 +1,9 @@ LIST OF CHANGES - Removed the use of 'xml' lims driver from all tests. - - Deleted 'xml' lims driver class and all classes, which supported this + - Deleted 'xml' lims driver class and all classes which supported this functionality, together with all related tests and test data. - - In release 97.0.0, ihe default LIMS driver type in samplesheet generation + - In release 97.0.0, the default LIMS driver type in samplesheet generation was changed to 'ml_warehouse'. Following this change, the code for auto-generation of MiSeq default samplesheets is now simplified to exclude an explicit creation of LIMS objects. @@ -11,7 +11,7 @@ LIST OF CHANGES removal: - deleted all previously deprecated methods ('seq_qc_state', 'associated_lims', 'associated_child_lims', 'associated_child_lims_ia'); - - deleted methods, for which we do not have data in ml warehouse, our + - deleted methods for which we do not have data in ml warehouse, our primary source of LIMS data ('request_id', 'project_id', 'project_name'); - deleted all code for computing inline tag indexes and inferring tag sequences and library types from sample description since @@ -19,7 +19,7 @@ LIST OF CHANGES - reimplemented the 'reference_genome' method to exclude a fallback to a study reference for tag zero and lane-level objects when samples have different references. - - Restricted the 'all_lanes_mergeable' flag in the 'lonf_info' role to + - Restricted the 'all_lanes_mergeable' flag in the 'long_info' role to NovaSeq Standard workflow, ie dropped an additional case of HiSeq Rapid Run since HiSeq instruments are no longer used. - Updated DBIx classes from the prod database. Changes are due to the MySQL