From 71abfbb576c5847e6d9a30119aec0a3d256500d4 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 22 Sep 2023 09:34:22 +0100 Subject: [PATCH] Simplified samplesheet auto-generation code. Recently, 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. --- lib/npg/samplesheet/auto.pm | 16 +++------------- 1 file changed, 3 insertions(+), 13 deletions(-) diff --git a/lib/npg/samplesheet/auto.pm b/lib/npg/samplesheet/auto.pm index 3a4b479d..bcc061e9 100644 --- a/lib/npg/samplesheet/auto.pm +++ b/lib/npg/samplesheet/auto.pm @@ -11,7 +11,6 @@ use File::Spec::Functions; use npg::samplesheet; use npg_tracking::Schema; use WTSI::DNAP::Warehouse::Schema; -use st::api::lims; use st::api::lims::samplesheet; with q(MooseX::Log::Log4perl); @@ -107,17 +106,10 @@ sub process { my $id_run = $r->id_run; $self->log->info('Considering ' . join q[,],$id_run,$r->instrument->name); - my $l = st::api::lims->new( - position => 1, - id_run => $id_run, - id_flowcell_lims => $r->batch_id, - driver_type => q(ml_warehouse), - mlwh_schema => $self->mlwh_schema + my $ss = npg::samplesheet->new( + run => $r, mlwh_schema => $self->mlwh_schema ); - - my $ss = npg::samplesheet->new(run => $r, lims => [$l]); - - my$o=$ss->output; + my $o = $ss->output; my $generate_new = 1; if(-e $o) { @@ -228,8 +220,6 @@ __END__ =item npg::samplesheet -=item st:api::lims - =item st::api::lims::samplesheet =item WTSI::DNAP::Warehouse::Schema