Merge pull request #469 from ces/pacbio27

Pacbio - just code reorganisation
wtsi-npg · Sep 24, 2024 · ff64271 · ff64271
2 parents 2c7e1a2 + f2f1156
commit ff64271
Show file tree

Hide file tree

Showing 532 changed files with 794 additions and 838 deletions.
diff --git a/MANIFEST b/MANIFEST
diff --git a/bin/npg_pacbio_analysis_monitor.pl b/bin/npg_pacbio_analysis_monitor.pl
@@ -13,7 +13,7 @@
 
 use WTSI::DNAP::Warehouse::Schema;
 use WTSI::NPG::iRODS;
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitor;
+use WTSI::NPG::HTS::PacBio::AnalysisMonitor;
 
 our $VERSION = '';
 

diff --git a/bin/npg_pacbio_run_auxiliary.pl b/bin/npg_pacbio_run_auxiliary.pl
@@ -13,8 +13,8 @@
 
 use WTSI::DNAP::Warehouse::Schema;
 use WTSI::NPG::DriRODS;
-use WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitor;
-use WTSI::NPG::HTS::PacBio::Sequel::RunAuditor;
+use WTSI::NPG::HTS::PacBio::RunDeleteMonitor;
+use WTSI::NPG::HTS::PacBio::RunAuditor;
 
 our $VERSION = '';
 

diff --git a/bin/npg_pacbio_runmonitor.pl b/bin/npg_pacbio_runmonitor.pl
@@ -13,7 +13,7 @@
 
 use WTSI::DNAP::Warehouse::Schema;
 use WTSI::NPG::iRODS;
-use WTSI::NPG::HTS::PacBio::Sequel::RunMonitor;
+use WTSI::NPG::HTS::PacBio::RunMonitor;
 
 
 our $VERSION = '';

diff --git a/bin/npg_publish_pacbio_run.pl b/bin/npg_publish_pacbio_run.pl
@@ -11,7 +11,7 @@
 
 use WTSI::DNAP::Warehouse::Schema;
 use WTSI::NPG::iRODS;
-use WTSI::NPG::HTS::PacBio::Sequel::RunPublisher;
+use WTSI::NPG::HTS::PacBio::RunPublisher;
 
 our $VERSION = '';
 

diff --git a/.../NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm → lib/WTSI/NPG/HTS/PacBio/AnalysisMonitor.pm b/.../NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm → lib/WTSI/NPG/HTS/PacBio/AnalysisMonitor.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitor;
+package WTSI::NPG::HTS::PacBio::AnalysisMonitor;
 
 use namespace::autoclean;
 use DateTime;
@@ -8,13 +8,12 @@ use MooseX::StrictConstructor;
 use Readonly;
 use Try::Tiny;
 
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher;
-use WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher;
+use WTSI::NPG::HTS::PacBio::AnalysisPublisher;
+use WTSI::NPG::HTS::PacBio::IsoSeqPublisher;
 
 with qw[
          WTSI::DNAP::Utilities::Loggable
          WTSI::NPG::HTS::PacBio::MonitorBase
-         WTSI::NPG::HTS::PacBio::Sequel::MonitorBase
        ];
 
 our $VERSION = '';
@@ -122,7 +121,7 @@ sub _publish_analysis_path {
     push @init_args, dest_collection => $self->dest_collection;
   }
 
-  my $publisher = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new(@init_args);
+  my $publisher = WTSI::NPG::HTS::PacBio::AnalysisPublisher->new(@init_args);
 
   return $publisher->publish_files();
 }
@@ -145,7 +144,7 @@ sub _publish_iso_analysis_path {
 
   push @init_args, analysis_id => $job->{id};
 
-  my $publisher = WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher->new(@init_args);
+  my $publisher = WTSI::NPG::HTS::PacBio::IsoSeqPublisher->new(@init_args);
 
   return $publisher->publish_files();
 }
@@ -161,7 +160,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitor
+WTSI::NPG::HTS::PacBio::AnalysisMonitor
 
 =head1 DESCRIPTION
 

diff --git a/...PG/HTS/PacBio/Sequel/AnalysisPublisher.pm → lib/WTSI/NPG/HTS/PacBio/AnalysisPublisher.pm b/...PG/HTS/PacBio/Sequel/AnalysisPublisher.pm → lib/WTSI/NPG/HTS/PacBio/AnalysisPublisher.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher;
+package WTSI::NPG::HTS::PacBio::AnalysisPublisher;
 
 use namespace::autoclean;
 use English qw[-no_match_vars];
@@ -10,9 +10,9 @@ use MooseX::StrictConstructor;
 use Perl6::Slurp;
 use Readonly;
 
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport;
-use WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
-use WTSI::NPG::HTS::PacBio::Sequel::Product;
+use WTSI::NPG::HTS::PacBio::AnalysisReport;
+use WTSI::NPG::HTS::PacBio::MetaXMLParser;
+use WTSI::NPG::HTS::PacBio::Product;
 
 with qw[
          WTSI::NPG::HTS::PacBio::PublisherBase
@@ -46,7 +46,7 @@ Readonly::Scalar my $HUNDRED       => 100;
 Readonly::Scalar my $MIN_BARCODED  => 0.8;
 Readonly::Scalar my $BARCODE_FIELD => 'Percent Barcoded Reads';
 Readonly::Scalar my $REPORT_TITLE  =>
-  $WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport::REPORTS;
+  $WTSI::NPG::HTS::PacBio::AnalysisReport::REPORTS;
 Readonly::Scalar my $LIMA_SUMMARY  => 'lima.summary.txt';
 
 
@@ -138,7 +138,7 @@ sub publish_sequence_files {
 
   my ($num_files, $num_processed, $num_errors) = (0, 0, 0);
 
-  my $product = WTSI::NPG::HTS::PacBio::Sequel::Product->new();
+  my $product = WTSI::NPG::HTS::PacBio::Product->new();
 
   foreach my $file ( @{$files} ){
     my @tag_records;
@@ -318,7 +318,7 @@ sub _build_merged_report {
                    runfolder_path => $self->runfolder_path,
                    meta_data      => $self->_metadata);
 
-  my $report = WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport->new(@init_args);
+  my $report = WTSI::NPG::HTS::PacBio::AnalysisReport->new(@init_args);
   return $report->generate_analysis_report;
 }
 
@@ -422,7 +422,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher
+WTSI::NPG::HTS::PacBio::AnalysisPublisher
 
 =head1 DESCRIPTION
 

diff --git a/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherBase.pm b/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherBase.pm
@@ -4,7 +4,7 @@ use File::Spec::Functions qw[catdir];
 use Moose::Role;
 use MooseX::StrictConstructor;
 use WTSI::NPG::HTS::PacBio::Metadata;
-use WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
+use WTSI::NPG::HTS::PacBio::MetaXMLParser;
 
 our $VERSION = '';
 
@@ -55,7 +55,7 @@ sub _build_metadata{
     $self->logcroak('Metadata files is not defined for '. $self->analysis_path);
   }
 
-  return  WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file
+  return  WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file
                  ($self->_metadata_file, $METADATA_PREFIX);
 }
 

diff --git a/...I/NPG/HTS/PacBio/Sequel/AnalysisReport.pm → lib/WTSI/NPG/HTS/PacBio/AnalysisReport.pm b/...I/NPG/HTS/PacBio/Sequel/AnalysisReport.pm → lib/WTSI/NPG/HTS/PacBio/AnalysisReport.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport;
+package WTSI::NPG::HTS::PacBio::AnalysisReport;
 
 use namespace::autoclean;
 use File::Basename;
@@ -11,7 +11,7 @@ use Perl6::Slurp;
 use Readonly;
 use XML::LibXML;
 
-use WTSI::NPG::HTS::PacBio::Sequel::Reportdata;
+use WTSI::NPG::HTS::PacBio::Reportdata;
 
 with qw[
          WTSI::DNAP::Utilities::Loggable
@@ -147,7 +147,7 @@ sub _save_results {
     %files = map { $_ => $self->_get_result($_) } $self->_get_result_keys;
   }
 
-  my $data = WTSI::NPG::HTS::PacBio::Sequel::Reportdata->new
+  my $data = WTSI::NPG::HTS::PacBio::Reportdata->new
     (meta_data => $self->meta_data,
      $REPORTS  => \%files );
 
@@ -169,7 +169,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport
+WTSI::NPG::HTS::PacBio::AnalysisReport
 
 =head1 DESCRIPTION
 

diff --git a/...TSI/NPG/HTS/PacBio/Sequel/ImageArchive.pm → lib/WTSI/NPG/HTS/PacBio/ImageArchive.pm b/...TSI/NPG/HTS/PacBio/Sequel/ImageArchive.pm → lib/WTSI/NPG/HTS/PacBio/ImageArchive.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::ImageArchive;
+package WTSI::NPG::HTS::PacBio::ImageArchive;
 
 use namespace::autoclean;
 use File::Basename;
@@ -168,7 +168,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::ImageArchive
+WTSI::NPG::HTS::PacBio::ImageArchive
 
 =head1 DESCRIPTION
 

diff --git a/.../NPG/HTS/PacBio/Sequel/IsoSeqPublisher.pm → lib/WTSI/NPG/HTS/PacBio/IsoSeqPublisher.pm b/.../NPG/HTS/PacBio/Sequel/IsoSeqPublisher.pm → lib/WTSI/NPG/HTS/PacBio/IsoSeqPublisher.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher;
+package WTSI::NPG::HTS::PacBio::IsoSeqPublisher;
 
 use namespace::autoclean;
 use DateTime;
@@ -15,8 +15,8 @@ use Readonly;
 use Try::Tiny;
 use XML::LibXML;
 
-use WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
-use WTSI::NPG::HTS::PacBio::Sequel::Product;
+use WTSI::NPG::HTS::PacBio::MetaXMLParser;
+use WTSI::NPG::HTS::PacBio::Product;
 use WTSI::DNAP::Utilities::Runnable;
 
 with qw[
@@ -197,7 +197,7 @@ sub publish_sequence_files {
 
   my ($num_files, $num_processed, $num_errors) = (0, 0, 0);
 
-  my $product = WTSI::NPG::HTS::PacBio::Sequel::Product->new();
+  my $product = WTSI::NPG::HTS::PacBio::Product->new();
 
   foreach my $file ( @{$files} ){
 
@@ -368,7 +368,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher
+WTSI::NPG::HTS::PacBio::IsoSeqPublisher
 
 =head1 DESCRIPTION
 

diff --git a/...SI/NPG/HTS/PacBio/Sequel/MetaXMLParser.pm → lib/WTSI/NPG/HTS/PacBio/MetaXMLParser.pm b/...SI/NPG/HTS/PacBio/Sequel/MetaXMLParser.pm → lib/WTSI/NPG/HTS/PacBio/MetaXMLParser.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
+package WTSI::NPG::HTS::PacBio::MetaXMLParser;
 
 use namespace::autoclean;
 use Moose;
@@ -145,7 +145,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser
+WTSI::NPG::HTS::PacBio::MetaXMLParser
 
 =head1 DESCRIPTION
 

diff --git a/lib/WTSI/NPG/HTS/PacBio/MonitorBase.pm b/lib/WTSI/NPG/HTS/PacBio/MonitorBase.pm
@@ -33,6 +33,36 @@ has 'mlwh_schema' =>
    required      => 1,
    documentation => 'A ML warehouse handle to obtain secondary metadata');
 
+has 'api_client' =>
+  (isa           => 'WTSI::NPG::HTS::PacBio::Sequel::APIClient',
+   is            => 'ro',
+   lazy_build    => 1,
+   builder       => q[_build_api_client],
+   documentation => 'A PacBio Sequel API client used to fetch runs');
+
+sub _build_api_client {
+    my $self = shift;
+    my @init_args = $self->api_uri ? ('api_uri' => $self->api_uri) : ();
+    if($self->interval) { push @init_args, ('default_interval' => $self->interval) };
+    if($self->older_than) { push @init_args, ('default_end' => $self->older_than) };
+    return WTSI::NPG::HTS::PacBio::Sequel::APIClient->new(@init_args);
+}
+
+has 'api_uri' =>
+  (isa           => 'Str',
+   is            => 'ro',
+   documentation => 'PacBio root API URL');
+
+has 'interval' =>
+  (isa           => 'Str',
+   is            => 'ro',
+   documentation => 'Interval of time in days');
+
+has 'older_than' =>
+  (isa           => 'Str',
+   is            => 'ro',
+   documentation => 'Time in days to remove from end date');
+
 
 no Moose::Role;
 

diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/Product.pm → lib/WTSI/NPG/HTS/PacBio/Product.pm b/lib/WTSI/NPG/HTS/PacBio/Sequel/Product.pm → lib/WTSI/NPG/HTS/PacBio/Product.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::Product;
+package WTSI::NPG::HTS::PacBio::Product;
 
 use Moose;
 use English qw[-no_match_vars];
@@ -76,7 +76,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::Product
+WTSI::NPG::HTS::PacBio::Product
 
 =head1 DESCRIPTION
 

diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/Reportdata.pm → lib/WTSI/NPG/HTS/PacBio/Reportdata.pm b/lib/WTSI/NPG/HTS/PacBio/Sequel/Reportdata.pm → lib/WTSI/NPG/HTS/PacBio/Reportdata.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::Reportdata;
+package WTSI::NPG::HTS::PacBio::Reportdata;
 
 use namespace::autoclean;
 use DateTime;
@@ -60,7 +60,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::Reportdata
+WTSI::NPG::HTS::PacBio::Reportdata
 
 =head1 DESCRIPTION
 

diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditor.pm → lib/WTSI/NPG/HTS/PacBio/RunAuditor.pm b/lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditor.pm → lib/WTSI/NPG/HTS/PacBio/RunAuditor.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunAuditor;
+package WTSI::NPG::HTS::PacBio::RunAuditor;
 
 use namespace::autoclean;
 use English qw[-no_match_vars];
@@ -17,8 +17,7 @@ Readonly::Scalar my $MODE_GROUP_WRITABLE => 0020;
 with qw[
          WTSI::DNAP::Utilities::Loggable
          WTSI::NPG::HTS::PacBio::MonitorBase
-         WTSI::NPG::HTS::PacBio::Sequel::MonitorBase
-         WTSI::NPG::HTS::PacBio::Sequel::RunPublisherBase
+         WTSI::NPG::HTS::PacBio::RunPublisherBase
        ];
 
 our $VERSION = '';
@@ -184,7 +183,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::RunAuditor
+WTSI::NPG::HTS::PacBio::RunAuditor
 
 =head1 DESCRIPTION
 

diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDelete.pm → lib/WTSI/NPG/HTS/PacBio/RunDelete.pm b/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDelete.pm → lib/WTSI/NPG/HTS/PacBio/RunDelete.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunDelete;
+package WTSI::NPG::HTS::PacBio::RunDelete;
 
 use namespace::autoclean;
 use Moose;
@@ -61,7 +61,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::RunDelete
+WTSI::NPG::HTS::PacBio::RunDelete
 
 =head1 DESCRIPTION