Simplifies the default samplesheet path.

An option to read the value from the configuration file is not used.
wtsi-npg · Dec 18, 2023 · 86531f4 · 86531f4
1 parent a5a1ce3
commit 86531f4
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Showing 3 changed files with 4 additions and 15 deletions.
diff --git a/lib/npg/samplesheet/base.pm b/lib/npg/samplesheet/base.pm
@@ -8,7 +8,6 @@ use MooseX::Getopt::Meta::Attribute::Trait::NoGetopt;
 
 use npg_tracking::Schema;
 use st::api::lims;
-use npg_tracking::util::config qw(get_config_staging_areas);
 use WTSI::DNAP::Warehouse::Schema;
 
 with 'npg_tracking::glossary::run';
@@ -31,8 +30,7 @@ A parent class for samplesheet generator. Provides common attributes.
 
 =cut
 
-my$config=get_config_staging_areas();
-Readonly::Scalar my $SAMPLESHEET_PATH => $config->{'samplesheets'}||q(samplesheets/);
+Readonly::Scalar my $SAMPLESHEET_PATH => 'samplesheets/';
 Readonly::Scalar my $LIMS_DRIVER_TYPE => 'ml_warehouse';
 
 =head1 SUBROUTINES/METHODS
@@ -221,8 +219,6 @@ __END__
 
 =item  st::api::lims
 
-=item npg_tracking::util::config
-
 =item npg_tracking::glossary::run
 
 =back

diff --git a/t/.npg/npg_tracking b/t/.npg/npg_tracking
@@ -3,7 +3,6 @@ my $VAR1 = {
   'staging_areas' => {
     'indexes' => [18 .. 32, 34 .. 47, 49 .. 55],
     'prefix' => '/nfs/sf',
-    'samplesheets' => '/nfs/sf49/ILorHSorMS_sf49/samplesheets/'
   },
   'staging_areas2webservers' => {
     'gs01'    => {'npg_tracking' => 'http://gso1.san.ac.uk:678',

diff --git a/t/47-samplesheet.t b/t/47-samplesheet.t
@@ -10,7 +10,6 @@ use Moose::Meta::Class;
 
 use t::dbic_util;
 local $ENV{'dev'} = q(wibble);
-local $ENV{'HOME'} = q(t/);
 
 use_ok('npg::samplesheet');
 use_ok('st::api::lims');
@@ -22,8 +21,6 @@ my $mlwh_schema = $class->new_object({})->create_test_db(
   q[WTSI::DNAP::Warehouse::Schema], q[t/data/fixtures_lims_wh_samplesheet]
 );
 
-local $ENV{NPG_WEBSERVICE_CACHE_DIR} = q(t/data/samplesheet);
-
 my $dir = tempdir( CLEANUP => 1 );
 
 subtest 'simple tests for the default driver' => sub {
@@ -51,22 +48,19 @@ subtest 'object creation' => sub {
   lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema,
     repository=>$dir, npg_tracking_schema=>$schema, id_run=>7007); }
     'samplesheet object - no output provided';
-  cmp_ok($ss->output, 'eq',
-    '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/MS0001309-300.csv',
+  cmp_ok($ss->output, 'eq', 'samplesheets/wibble/MS0001309-300.csv',
     'default output location (with zeroes trimmed appropriately)');
 
   lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema,
     repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946); }
     'samplesheet object - no output provided';
-  cmp_ok($ss->output, 'eq',
-    '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/000000000-A0616.csv',
+  cmp_ok($ss->output, 'eq', 'samplesheets/wibble/000000000-A0616.csv',
     'default output location');
 
   lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, repository=>$dir, npg_tracking_schema=>$schema, id_run=>7007); } 'samplesheet object - no output provided';
   my $orig_flowcell_id = $ss->run->flowcell_id;
   $ss->run->flowcell_id(q(MS2000132-500V2));
-  cmp_ok($ss->output, 'eq',
-    '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/MS2000132-500V2.csv',
+  cmp_ok($ss->output, 'eq', 'samplesheets/wibble/MS2000132-500V2.csv',
     'default output location copes with V2 MiSeq cartirdges/reagent kits');
 };