Merge pull request #570 from wtsi-npg/devel

merge from devel to master to create release 91.1.0

Author: mgcam

Changes

@@ -1,5 +1,12 @@
 LIST OF CHANGES
 
+release 91.1.0
+ - staging monitor changes for SP flowcells
+ - Update URL for production Sequencescape LIMS
+ - method for creating a lane-level st::api::lims object from
+   any other st::api::lims object where the resulting object has
+   the same driver as the original one
+
 release 91.0.0
  - modified is_i5opposite when there is no reverse read
  - removed scripts for monitoring instruments via ftp; related

lib/Monitor/RunFolder/Staging.pm

@@ -31,7 +31,6 @@ Readonly::Scalar my $RTA_COMPLETE         => 10 * $SECONDS_PER_MINUTE;
 Readonly::Scalar my $INTENSITIES_DIR_PATH => 'Data/Intensities';
 Readonly::Array  my @NO_MOVE_NAMES        => qw( npgdonotmove npg_do_not_move );
 Readonly::Scalar my $MODE_INDEX           => 2;
-Readonly::Scalar my $EXP_CBCLS_PER_CYCL   => 2;
 
 Readonly::Scalar my $RTA_COMPLETE_FN      => q[RTAComplete\.txt];
 Readonly::Scalar my $COPY_COMPLETE_FN     => q[CopyComplete\.txt];
@@ -159,10 +158,11 @@ sub monitor_stats {
 sub check_tiles {
     my ($self) = @_;
 
-    my $expected_lanes  = $self->lane_count();
-    my $expected_cycles = $self->expected_cycle_count();
-    my $expected_tiles  = $self->lane_tilecount();
-    my $path            = $self->runfolder_path();
+    my $expected_lanes    = $self->lane_count();
+    my $expected_surfaces = $self->surface_count();
+    my $expected_cycles   = $self->expected_cycle_count();
+    my $expected_tiles    = $self->lane_tilecount();
+    my $path              = $self->runfolder_path();
 
     print {*STDERR} "\tChecking Lanes, Cycles, Tiles...\n" or carp $OS_ERROR;
 
@@ -216,9 +216,10 @@ sub check_tiles {
                 my @cbcl_files = glob "$cycle/*.$filetype" . q({,.gz});
                 @cbcl_files = grep { m/ L \d+ _ \d+ [.] $filetype (?: [.] gz )? $ /msx } @cbcl_files;
                 my $count = scalar @cbcl_files;
-                if ( $count != $EXP_CBCLS_PER_CYCL ) {
+                # there should be one cbcl file per expected surface
+                if ( $count != $expected_surfaces ) {
                     carp 'Missing cbcl(s) files: '
-                       . "$cycle - [expected: $EXP_CBCLS_PER_CYCL, found: $count]";
+                       . "$cycle - [expected: $expected_surfaces, found: $count]";
                     return 0;
                 }
             } else {

lib/npg/api/request.pm

@@ -209,10 +209,10 @@ sub make {
 sub _create_path {
   my ( $self, $url ) = @_;
 
-  my ($stpath)  = $url =~ m{\Ahttps?://(?:dev\.)?
+  my ($stpath)  = $url =~ m{\Ahttps?://(?:(?:dev|sequencescape)\.)?
                             psd.*
-                            \.sanger\.ac\.uk?(?::\d+)
-                            (.*?)\z}xms; # sequencescape path
+                            \.sanger\.ac\.uk?(?::\d+)?
+                            (/.*?)\z}xms; # sequencescape path
   ##no critic(ProhibitComplexRegexes)
   my ($npgpath) = $url =~ m{\Ahttps?://
                             (?:npg|sfweb|sf2-farm-srv1)
@@ -469,7 +469,7 @@ Marina Gourtovaia
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2010 GRL, by Marina Gourtovaia
+Copyright (C) 2010,2020 Genome Research Ltd. by Marina Gourtovaia
 
 This file is part of NPG.
 

lib/npg/util.pm

@@ -160,7 +160,7 @@ Marina Gourtovaia
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2018 GRL
+Copyright (C) 2018,2020 Genome Research Ltd.
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by

lib/npg_tracking/illumina/run/long_info.pm

@@ -120,6 +120,22 @@ has q{lane_count} => (
   documentation => q{The number of lanes on this run},
 );
 
+=head2 surface_count
+
+Number of surfaces configured for this run. May be set on Construction.
+
+  my $iSurfaceCount = $self->surface_count();
+
+=cut
+
+has q{surface_count} => (
+  is            => 'ro',
+  isa           => 'Int',
+  writer        => '_set_surface_count',
+  predicate     => 'has_surface_count',
+  documentation => q{The number of surfaces on this run},
+);
+
 =head2 read_cycle_counts
 
 List of cycle lengths configured for each read/index in order.
@@ -388,6 +404,7 @@ sub _build_run_flowcell {
 
 foreach my $f ( qw(expected_cycle_count
                    lane_count
+                   surface_count 
                    read_cycle_counts
                    indexing_cycle_range
                    read1_cycle_range
@@ -510,6 +527,20 @@ sub _build_workflow_type {
   return _get_single_element_text($self->_run_params(), 'WorkflowType');
 }
 
+=head2 flowcell_mode
+
+=cut
+
+has q{flowcell_mode} => (
+  isa        => 'Str',
+  is         => 'ro',
+  lazy_build => 1,
+);
+sub _build_flowcell_mode {
+  my $self = shift;
+  return _get_single_element_text($self->_run_params(), 'FlowCellMode');
+}
+
 =head2 all_lanes_mergeable
 
 Method returns true if all lanes on the flowcell contain the
@@ -697,6 +728,9 @@ sub _build__runinfo_store {
 
   my $fcl_el = $doc->getElementsByTagName('FlowcellLayout')->[0];
   if(not defined $fcl_el) {
+    if ( $self->platform_NovaSeq() ) {
+      croak q{No FlowCellLayout for NovaSeq run};
+    }
     $self->_set_lane_count($doc->getElementsByTagName('Lane')->size);
     $self->_set_expected_cycle_count($doc->getElementsByTagName('Cycles')->[0]->getAttribute('Incorporation'));
 
@@ -725,7 +759,12 @@ sub _build__runinfo_store {
 
   }else{
     $self->_set_lane_count($fcl_el->getAttribute('LaneCount'));
-    my $ncol = $fcl_el->getAttribute('SurfaceCount') * $fcl_el->getAttribute('SwathCount');
+    $self->_set_surface_count($fcl_el->getAttribute('SurfaceCount'));
+    if ( $self->platform_NovaSeq() && $self->flowcell_mode() eq 'SP' ) {
+      # NovaSeq SP flowcells only have one surface
+      $self->_set_surface_count(1);
+    }
+    my $ncol = $self->surface_count() * $fcl_el->getAttribute('SwathCount');
     my $nrow = $fcl_el->getAttribute('TileCount'); #informatic split on HiSeq
     $self->_set_tilelayout_columns($ncol);
     $self->_set_tilelayout_rows($nrow);

lib/st/api/base.pm

@@ -13,7 +13,7 @@ use npg::api::util;
 
 our $VERSION = '0';
 
-sub live_url { return q{http://psd-support.internal.sanger.ac.uk:6600}; }
+sub live_url { return q{http://sequencescape.psd.sanger.ac.uk}; }
 sub dev_url  { return q{http://dev.psd.sanger.ac.uk:6610}; }
 
 sub lims_url {

lib/st/api/lims.pm

@@ -996,6 +996,29 @@ sub create_tag_zero_object {
   return __PACKAGE__->new(%init);
 }
 
+=head2 create_lane_object
+
+Using id_run and position values given as attributes to this method, creates
+and returns an st::api::lims object for the lane corresponding to the given
+attributes. The new object has the same driver settings as the original object.
+
+  my $l = st::api::lims->new(id_run => 4, position => 3, tag_index => 6);
+  my $lane_lims = $l->create_lane_object(4,4);
+
+=cut
+
+sub create_lane_object {
+  my ($self, $id_run, $position) = @_;
+  ($id_run and $position) or croak 'id_run and position are expected as arguments';
+  my %init = %{$self->_driver_arguments()};
+  $init{'driver_type'} = $self->driver_type;
+  delete $init{'tag_index'};
+  delete $init{'rpt_list'};
+  $init{'id_run'}   = $id_run;
+  $init{'position'} = $position;
+  return __PACKAGE__->new(%init);
+}
+
 =head2 cached_samplesheet_var_name
 
 Returns the name of the env. variable for storing the full path of the cached
@@ -1410,7 +1433,7 @@ Marina Gourtovaia E<lt>mg8@sanger.ac.ukE<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2018 Genome Research Ltd
+Copyright (C) 2013,2014,2015,2016,2017,2018,2019,2020 Genome Research Ltd.
 
 This file is part of NPG.
 

t/30-api-request.t

@@ -14,7 +14,7 @@ use npg::api::util;
 use st::api::sample;
 
 use t::useragent;
-my $lims_url = q[http://psd-support.internal.sanger.ac.uk:6600];
+my $lims_url = q[http://sequencescape.psd.sanger.ac.uk];
 my $ua = t::useragent->new({
                          is_success => 1,
                          mock       => {

t/34-monitor-runfolder.t

@@ -99,6 +99,14 @@ my $dir4rf = tempdir( CLEANUP => 1 );
   </RunInfo>
 ENDXML
     close $fh;
+    my $runparametersfile = qq[$fs_run_folder/runParameters.xml];
+    open($fh, '>', $runparametersfile) or die "Could not open file '$runparametersfile' $!";
+    print $fh <<"ENDXML";
+<?xml version="1.0"?>
+  <RunParameters xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  </RunParameters>
+ENDXML
+    close $fh;
 
     my $test = Monitor::RunFolder->new( runfolder_path      => $fs_run_folder,
                                         npg_tracking_schema => $schema, );
@@ -135,6 +143,14 @@ ENDXML
   </RunInfo>
 ENDXML
     close $fh2;
+    my $runparametersfile2= qq[$fs_run_folder2/runParameters.xml];
+    open($fh2, '>', $runparametersfile2) or die "Could not open file '$runparametersfile2' $!";
+    print $fh2 <<"ENDXML";
+<?xml version="1.0"?>
+  <RunParameters xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  </RunParameters>
+ENDXML
+    close $fh2;
 
     $test = Monitor::RunFolder->new( runfolder_path      => $fs_run_folder2,
                                      npg_tracking_schema => $schema, );
@@ -166,6 +182,10 @@ q{<?xml version="1.0"?>
     </AlignToPhiX>
   </Run>
 </RunInfo>};
+    my $run_parameters = 
+q{<?xml version="1.0"?>
+<RunParameters xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+</RunParameters>};
 
 
     my $root = tempdir( CLEANUP => 1 );
@@ -186,6 +206,11 @@ q{<?xml version="1.0"?>
     print $fh $run_info;
     close $fh;
 
+    # create runParameters file
+    open my $fh2, '>', join(q[/], $rf, 'runParameters.xml');
+    print $fh2 $run_parameters;
+    close $fh2;
+
     warnings_like { $test->delete_superfluous_lanes() } [
       qr/Deleted lane 3/, qr/Deleted lane 4/, qr/Deleted lane 5/,
       qr/Deleted lane 6/, qr/Deleted lane 7/, qr/Deleted lane 8/],

t/40-st-base.t

@@ -7,7 +7,7 @@ use_ok('st::api::base');
 {
   my $base = st::api::base->new();
   isa_ok($base, 'st::api::base');
-  like($base->live_url(), qr/psd\-support/, 'live_url');
+  like($base->live_url(), qr/sequencescape[.]psd/, 'live_url');
   like($base->dev_url(), qr/dev\.psd/, 'dev_url');
   is((scalar $base->fields()), undef, 'no default fields');
   is($base->primary_key(), undef, 'no default pk');