Merge pull request #835 from wtsi-npg/devel

pull from devel to master to create release 68.1.0

Changes

@@ -1,6 +1,12 @@
 LIST OF CHANGES
 ---------------
 
+release 68.1.0
+ - Apply changes to the code and tests, which follow from removing some
+   functionality from npg_tracking::illumina::runfolder, see
+   https://github.com/wtsi-npg/npg_tracking/pull/807. The pipeline retains
+   all its previous functionality.
+
 release 68.0.0
  - Use st::api::lims->aggregate_libraries() method for both 'merge_lanes' and
    'merge_by_library' pipeline options. This is a breaking change as far as

lib/npg_pipeline/base.pm

@@ -26,16 +26,12 @@ with qw{
        };
 
 Readonly::Array my @NO_SCRIPT_ARG_ATTRS  => qw/
-                                               slot
-                                               instrument_string
                                                subpath
                                                tilelayout_rows
                                                tile_count
                                                lane_tilecount
                                                tilelayout_columns
                                                npg_tracking_schema
-                                               flowcell_id
-                                               name
                                                tracking_run
                                                experiment_name
                                                logger
@@ -60,8 +56,6 @@ within npg_pipeline package
 
 =head2 npg_tracking_schema
 
-=head2 flowcell_id
-
 =head2 tracking_run
 
 =head2 logger

t/00-distribution.t

@@ -10,8 +10,6 @@ eval {
 if($EVAL_ERROR) {
   plan skip_all => 'Test::Distribution not installed';
 } else {
-  my @nots = qw(prereq pod);
-  local $ENV{'PATH'} = join q[:], 't/bin', $ENV{'PATH'};
   Test::Distribution->import(only => [qw/versions description/], distversion => 1);
 }
 

t/00-podcoverage.t

@@ -4,7 +4,6 @@ use Test::More;
 
 eval "use Test::Pod::Coverage 1.00";
 plan skip_all => "Test::Pod::Coverage 1.00 required for testing POD coverage" if $@;
-local $ENV{'PATH'} = join q[:], 't/bin', $ENV{'PATH'};
 all_pod_coverage_ok();
 
 1;

t/10-base.t

@@ -1,15 +1,14 @@
 use strict;
 use warnings;
-use Test::More tests => 9;
+use Test::More tests => 8;
 use Test::Exception;
 use File::Temp qw(tempdir tempfile);
-use Cwd;
+use Cwd qw(getcwd abs_path);
 use Log::Log4perl qw(:levels);
 use Moose::Util qw(apply_all_roles);
 use File::Copy qw(cp);
 
 use t::util;
-use npg_tracking::util::abs_path qw(abs_path);
 
 my $util = t::util->new();
 
@@ -54,25 +53,6 @@ subtest 'config' => sub {
     'Croaks for non-esistent config file as expected';
 };
 
-subtest 'flowcell id and barcode' => sub {
-  plan tests => 7;
-
-  my $bpath = t::util->new()->temp_directory;
-  my $path = join q[/], $bpath, '150206_HS29_15467_A_C5WL2ACXX';
-  my $base;
-  lives_ok { $base = npg_pipeline::base->new(runfolder_path => $path); }
-    'can create object without supplying run id';
-  is ($base->id_run, 15467, 'id run derived correctly from runfolder_path');
-  ok (!defined $base->id_flowcell_lims, 'lims flowcell id undefined');
-  is ($base->flowcell_id, 'C5WL2ACXX', 'flowcell barcode derived from runfolder path');
-
-  $path = join q[/], $bpath, '150204_MS8_15441_A_MS2806735-300V2';
-  $base = npg_pipeline::base->new(runfolder_path => $path, id_flowcell_lims => 45);
-  is ($base->id_run, 15441, 'id run derived correctly from runfolder_path');
-  is ($base->id_flowcell_lims, 45, 'lims flowcell id returned correctly');
-  is ($base->flowcell_id, 'MS2806735-300V2', 'MiSeq reagent kit id derived from runfolder path');
-};
-
 subtest 'repository preexec' => sub {
   plan tests => 1;
 

t/10-pluggable-central.t

@@ -5,8 +5,8 @@ use Test::Exception;
 use Log::Log4perl qw(:levels);
 use File::Copy qw(cp);
 use File::Path qw(make_path remove_tree);
+use Cwd qw(abs_path);
 
-use npg_tracking::util::abs_path qw(abs_path);
 use t::util;
 
 my $util = t::util->new();