Merge pull request #611 from rf9/1.16-rc2

Release for 1.16
wtsi-clarity · Jan 26, 2016 · 9fd2f3d · 9fd2f3d
2 parents 3927235 + 5d93b78
commit 9fd2f3d
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Showing 370 changed files with 40,070 additions and 8,627 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -75,6 +75,9 @@ install:
   - cpanm --quiet --notest URI::Escape
   - cpanm --quiet --notest POSIX
   - cpanm --quiet --notest UUID::Tiny
+  - cpanm --quiet --notest DBD::SQLite
+  - cpanm --quiet --notest DBD::mysql
+  - cpanm --quiet --notest DBI
   - cpanm --quiet --notest --no-lwp https://github.com/wtsi-npg/perl-dnap-utilities/releases/download/${DNAP_UTILITIES_VERSION}/WTSI-DNAP-Utilities-${DNAP_UTILITIES_VERSION}.tar.gz
   - cpanm --quiet --notest --no-lwp https://github.com/wtsi-npg/perl-rabbit-wrap/releases/download/${PERL_RABBIT_WRAP_VERSION}/WTSI-DNAP-RabbitMQ-${PERL_RABBIT_WRAP_VERSION}.tar.gz
 

diff --git a/src/perl/Build.PL b/src/perl/Build.PL
@@ -5,7 +5,7 @@ use Module::Build;
 my $class = Module::Build->subclass(code => <<'EOF');
 
   sub git_tag {
-    my $gitver = q[git describe --dirty --always];
+    my $gitver = q[git describe --tags --always];
     my $version = `$gitver` || 'unknown';
     $version =~ s/\s$//smxg;
     $version=~s/\A(?![\d])/0.0-/smx; #prepend 0.0- if does not start with a number
@@ -39,90 +39,92 @@ EOF
 
 my $builder = $class->new(
 
-          'module_name'         => 'wtsi_clarity',
-          'dist_author'         => 'WTSI, Seq. Informatics',
-          'dist_version'        => $class->git_tag(),
-          'dist_abstract'       => 'Custom scripting for GenoLogics (http://www.genologics.com) Clarity LIMS at WTSI',
-          'license'             => 'gpl',
+  'module_name'         => 'wtsi_clarity',
+  'dist_author'         => 'WTSI, Seq. Informatics',
+  'dist_version'        => $class->git_tag(),
+  'dist_abstract'       => 'Custom scripting for GenoLogics (http://www.genologics.com) Clarity LIMS at WTSI',
+  'license'             => 'gpl',
 
-          'configure_requires' => {
-                'ExtUtils::CBuilder'              => 0,
-          },
-
-          'build_requires' => {
-                'Module::Build'                   => 0,
-                'ExtUtils::CBuilder'              => 0,
-                'Test::Compile'                   => 0,
-                'Test::Distribution'              => 0,
-                'Test::Deep'                      => 0,
-                'Test::Exception'                 => 0,
-                'Test::MockObject::Extends'       => 0,
-                'Test::More'                      => 0,
-                'Test::Pod'                       => 0,
-                'Test::Pod::Coverage'             => 0,
-                'Test::Perl::Critic'              => 0,
-                'Test::Warn'                      => 0,
-                'File::Slurp'                     => 0,
-                'Cwd'                             => 0,
-          },
-
-          'requires'    => {
-                'AnyEvent'                        => 0,
-                'AnyEvent::RabbitMQ'              => 0,
-                'App::cpanminus'                  => 0,
-                'Carp'                            => 0,
-                'Config::Auto'                    => 0,
-                'Daemon::Control'                 => 0,
-                'DateTime'                        => 0,
-                'Digest::MD5'                     => 0,
-                'English'                         => 0,
-                'Exporter'                        => 0,
-                'Getopt::Long'                    => 0,
-                'File::Basename'                  => 0,
-                'File::Spec::Functions'           => 0,
-                'File::Copy'                      => 0,
-                'File::Copy::Recursive'           => 0,
-                'File::Path'                      => 0,
-                'File::Temp'                      => 0,
-                'FindBin'                         => 0,
-                'JSON'                            => 0,
-                'JSON::Any'                       => 0,
-                'JSON::Parse'                     => 0,
-                'HTTP::Request'                   => 0,
-                'lib'                             => 0,
-                'List::Compare'                   => 0,
-                'Log::Log4perl'                   => 0,
-                'LWP::UserAgent'                  => 0,
-                'Mojo::Collection'                => 0,
-                'Moose'                           => 0,
-                'Moose::Util::TypeConstraints'    => 0,
-                'MooseX::ClassAttribute'          => 0,
-                'MooseX::Getopt'                  => 0,
-                'MooseX::Getopt::Meta::Attribute::Trait::NoGetopt' => 0,
-                'MooseX::Storage'                 => 0,
-                'MooseX::Aliases'                 => 0,
-                'MooseX::StrictConstructor'       => 0,
-                'MooseX::Aliases'                 => 0,
-                'namespace::autoclean'            => 0,
-                'PDF::API2'                       => 0,
-                'PDF::Table'                      => '0.9.7',
-                'Net::SFTP::Foreign'              => 0,
-                'Readonly'                        => 0,
-                'strict'                          => 0,
-                'Text::CSV'                       => 0,
-                'Try::Tiny'                       => 0,
-                'warnings'                        => 0,
-                'XML::LibXML'                     => 2.0105,
-                'XML::SemanticDiff'               => 0,
-                'URI::Escape'                     => 0,
-                'POSIX'                           => 0,
-                'WTSI::DNAP::Utilities'           => '>= 0.4.2',
-                'WTSI::DNAP::RabbitMQ::Client'    => '>= 0.3.0',
-                'UUID::Tiny'                      => '>=1.04',
-
-          },
-
-          'dist'         => { COMPRESS => 'gzip', SUFFIX => 'gz', },
+  'configure_requires' => {
+    'ExtUtils::CBuilder'              => 0,
+  },
+  'build_requires' => {
+    'Module::Build'                   => 0,
+    'ExtUtils::CBuilder'              => 0,
+    'Test::Compile'                   => 0,
+    'Test::Distribution'              => 0,
+    'Test::Deep'                      => 0,
+    'Test::Exception'                 => 0,
+    'Test::MockObject::Extends'       => 0,
+    'Test::More'                      => 0,
+    'Test::Pod'                       => 0,
+    'Test::Pod::Coverage'             => 0,
+    'Test::Perl::Critic'              => 0,
+    'Test::Warn'                      => 0,
+    'File::Slurp'                     => 0,
+    'Cwd'                             => 0,
+  },
+  'requires' => {
+    'AnyEvent'                        => 0,
+    'AnyEvent::RabbitMQ'              => 0,
+    'App::cpanminus'                  => 0,
+    'Carp'                            => 0,
+    'Config::Auto'                    => 0,
+    'Daemon::Control'                 => 0,
+    'DateTime'                        => 0,
+    'DBD::SQLite'                     => 0,
+    'DBD::mysql'                      => 0,
+    'DBI'                             => 0,
+    'Digest::MD5'                     => 0,
+    'English'                         => 0,
+    'Exporter'                        => 0,
+    'File::Basename'                  => 0,
+    'File::Copy'                      => 0,
+    'File::Copy::Recursive'           => 0,
+    'File::Path'                      => 0,
+    'File::Spec::Functions'           => 0,
+    'File::Temp'                      => 0,
+    'FindBin'                         => 0,
+    'Getopt::Long'                    => 0,
+    'HTTP::Request'                   => 0,
+    'IPC::Open3'                      => 0,
+    'JSON'                            => 0,
+    'JSON::Any'                       => 0,
+    'JSON::Parse'                     => 0,
+    'lib'                             => 0,
+    'List::Compare'                   => 0,
+    'Log::Log4perl'                   => 0,
+    'LWP::UserAgent'                  => 0,
+    'Mojo::Collection'                => 0,
+    'Moose'                           => 0,
+    'Moose::Util::TypeConstraints'    => 0,
+    'MooseX::Aliases'                 => 0,
+    'MooseX::ClassAttribute'          => 0,
+    'MooseX::Getopt'                  => 0,
+    'MooseX::Getopt::Meta::Attribute::Trait::NoGetopt' => 0,
+    'MooseX::Storage'                 => 0,
+    'MooseX::StrictConstructor'       => 0,
+    'namespace::autoclean'            => 0,
+    'Net::SFTP::Foreign'              => 0,
+    'PDF::API2'                       => 0,
+    'PDF::Table'                      => '0.9.7',
+    'POSIX'                           => 0,
+    'Readonly'                        => 0,
+    'strict'                          => 0,
+    'Text::CSV'                       => 0,
+    'Try::Tiny'                       => 0,
+    'URI::Escape'                     => 0,
+    'UUID::Tiny'                      => '>=1.04',
+    'warnings'                        => 0,
+    'WTSI::DNAP::RabbitMQ::Client'    => '>= 0.3.0',
+    'WTSI::DNAP::Utilities'           => '>= 0.4.2',
+    'XML::LibXML'                     => 2.0105,
+    'XML::SemanticDiff'               => 0,
+  },
+  'dist' => {
+    COMPRESS => 'gzip',
+    SUFFIX => 'gz',
+  },
 );
 
 $builder->create_build_script();

diff --git a/src/perl/MANIFEST b/src/perl/MANIFEST
@@ -70,9 +70,6 @@ lib/wtsi_clarity/util/csv/factory.pm
 lib/wtsi_clarity/util/filename.pm
 lib/wtsi_clarity/util/label.pm
 lib/wtsi_clarity/util/pdf/factory/pico_analysis_results.pm
-lib/wtsi_clarity/util/pdf/factory.pm
-lib/wtsi_clarity/util/pdf/layout/pico_analysis_results.pm
-lib/wtsi_clarity/util/pdf/layout/worksheet.pm
 lib/wtsi_clarity/util/pdf/pdf_generator.pm
 lib/wtsi_clarity/util/print.pm
 lib/wtsi_clarity/util/report.pm

diff --git a/src/perl/bin/consumer b/src/perl/bin/consumer
@@ -0,0 +1,28 @@
+#! /usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin qw($Bin);
+use lib ( -d "$Bin/../lib/perl5" ? "$Bin/../lib/perl5" : "$Bin/../lib" );
+
+use wtsi_clarity::util::config;
+use wtsi_clarity::mq::consumer;
+
+sub start_consumer {
+  my ($consumer_name, $prefix, $message_handler) = @_;
+  my $config = wtsi_clarity::util::config->new();
+  my $config_section = "${prefix}_consumer";
+
+  wtsi_clarity::mq::consumer->new(
+    name            => $consumer_name,
+    pid_file        => $config->dir_path . "/${prefix}_pid",
+    stderr_file     => $config->dir_path . "/${prefix}_consumer.err",
+    stdout_file     => $config->dir_path . "/${prefix}_consumer.log",
+    queue           => $config->$config_section->{'queue'},
+    message_handler => $message_handler,
+  )->run();
+
+  return 1;
+}
+
+1;
diff --git a/src/perl/bin/event_message_consumer b/src/perl/bin/event_message_consumer
@@ -0,0 +1,16 @@
+#! /usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin qw($Bin);
+use lib ( -d "$Bin/../lib/perl5" ? ("$Bin/../lib/perl5", "$Bin"): ("$Bin/../lib", "$Bin") );
+
+use wtsi_clarity::mq::mh::event_message_handler;
+
+require qw{consumer};
+
+my $message_handler = wtsi_clarity::mq::mh::event_message_handler->new();
+
+start_consumer('Event Message Consumer', 'event', $message_handler);
+
+1;
diff --git a/src/perl/bin/message_consumer b/src/perl/bin/message_consumer
diff --git a/src/perl/bin/report_consumer b/src/perl/bin/report_consumer
@@ -3,21 +3,14 @@
 use strict;
 use warnings;
 use FindBin qw($Bin);
-use lib ( -d "$Bin/../lib/perl5" ? "$Bin/../lib/perl5" : "$Bin/../lib" );
+use lib ( -d "$Bin/../lib/perl5" ? ("$Bin/../lib/perl5", "$Bin"): ("$Bin/../lib", "$Bin") );
 
 use wtsi_clarity::mq::mh::report_message_handler;
-use wtsi_clarity::util::config;
-use wtsi_clarity::mq::consumer;
 
-my $config = wtsi_clarity::util::config->new();
+require qw{consumer};
 
-wtsi_clarity::mq::consumer->new(
-  name            => 'Report Message Consumer',
-  pid_file        => $config->dir_path . '/report_pid',
-  stderr_file     => $config->dir_path . '/report_message_consumer.err',
-  stdout_file     => $config->dir_path . '/report_message_consumer.log',
-  queue           => $config->report_consumer->{'queue'},
-  message_handler => wtsi_clarity::mq::mh::report_message_handler->new(),
-)->run();
+my $message_handler = wtsi_clarity::mq::mh::report_message_handler->new();
+
+start_consumer('Report Message Consumer', 'report', $message_handler);
 
 1;
diff --git a/src/perl/bin/unified_message_consumer b/src/perl/bin/unified_message_consumer
@@ -0,0 +1,16 @@
+#! /usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin qw($Bin);
+use lib ( -d "$Bin/../lib/perl5" ? ("$Bin/../lib/perl5", "$Bin"): ("$Bin/../lib", "$Bin") );
+
+use wtsi_clarity::mq::mh::unified_message_handler;
+
+require qw{consumer};
+
+my $message_handler = wtsi_clarity::mq::mh::unified_message_handler->new();
+
+start_consumer('Unified Warehouse Message Consumer', 'warehouse', $message_handler);
+
+1;