From 10e81fea56b221091b53698a1db91d1e51bca738 Mon Sep 17 00:00:00 2001 From: Carol Scott Date: Thu, 8 Aug 2024 19:44:50 +0100 Subject: [PATCH 1/2] Change to populate_wtsi_irods_groups.pl for empty data access groups --- Changes | 6 ++++++ bin/populate_wtsi_irods_groups.pl | 4 +++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/Changes b/Changes index 23dea99b..0c0c9a4a 100644 --- a/Changes +++ b/Changes @@ -1,3 +1,9 @@ +Unreleased + + - 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) diff --git a/bin/populate_wtsi_irods_groups.pl b/bin/populate_wtsi_irods_groups.pl index e18bc6be..0319295a 100755 --- a/bin/populate_wtsi_irods_groups.pl +++ b/bin/populate_wtsi_irods_groups.pl @@ -17,6 +17,8 @@ our $VERSION = ''; +Readonly::Scalar my $MANAGED_TYPE => q{managed}; + my $what_on_earth =<<'WOE'; Script to update WTSI iRODS systems with groups corresponding to @@ -163,7 +165,7 @@ sub _uid_to_irods_uid { @members = map { _uid_to_irods_uid($_) } map { @{ $group2uids->{$_} || [$_] } } @dags; } - elsif ($is_seq) { + elsif ($study->data_release_strategy ne $MANAGED_TYPE) { @members = @public; } else { From 736cdbd6ab13436e2e4fb075c0b282aa01cbe530 Mon Sep 17 00:00:00 2001 From: Carol Scott Date: Fri, 9 Aug 2024 11:33:18 +0100 Subject: [PATCH 2/2] Update help --- bin/populate_wtsi_irods_groups.pl | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/bin/populate_wtsi_irods_groups.pl b/bin/populate_wtsi_irods_groups.pl index 0319295a..ede3d342 100755 --- a/bin/populate_wtsi_irods_groups.pl +++ b/bin/populate_wtsi_irods_groups.pl @@ -40,11 +40,11 @@ and iRODS public group is used as the membership of the corresponding iRODS group. -If no data_access_group is set on the study, then if the study is -associated with sequencing the members of the iRODS group will be set -to the public group, else if the study is not associated with -sequencing tracked in the ML warehouse, the iRODS group will be left -empty (except for the iRODS groupadmin user). +If no data_access_group is set on the Sequencescape study, then if the +study doesn't have a data release type of managed the members of the +iRODS group will be set to the public group, else if the study has a +data release type of managed the iRODS group will be left empty (except +for the iRODS groupadmin user). Studies which are marked as have samples contaminated with human which should be removed will have an ss__human iRODS group created