Commit ba0f2590 authored by Leo Gordon's avatar Leo Gordon
Browse files

cosmetic: make it explicit that we are importing rearrange() and throw()

parent 5655fa32
...@@ -22,7 +22,7 @@ package Bio::EnsEMBL::Hive::Accumulator; ...@@ -22,7 +22,7 @@ package Bio::EnsEMBL::Hive::Accumulator;
use strict; use strict;
use Scalar::Util ('weaken'); use Scalar::Util ('weaken');
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()' use Bio::EnsEMBL::Utils::Argument ('rearrange');
sub new { sub new {
my $class = shift @_; my $class = shift @_;
......
...@@ -24,7 +24,8 @@ ...@@ -24,7 +24,8 @@
package Bio::EnsEMBL::Hive::Analysis; package Bio::EnsEMBL::Hive::Analysis;
use strict; use strict;
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()'
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
); );
......
...@@ -44,10 +44,11 @@ package Bio::EnsEMBL::Hive::AnalysisCtrlRule; ...@@ -44,10 +44,11 @@ package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
use strict; use strict;
use Scalar::Util ('weaken'); use Scalar::Util ('weaken');
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::URLFactory; use Bio::EnsEMBL::Hive::URLFactory;
use Bio::EnsEMBL::Hive::Extensions; use Bio::EnsEMBL::Hive::Extensions;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;
=head2 new =head2 new
......
...@@ -27,7 +27,8 @@ ...@@ -27,7 +27,8 @@
package Bio::EnsEMBL::Hive::AnalysisJob; package Bio::EnsEMBL::Hive::AnalysisJob;
use strict; use strict;
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()'
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Hive::Utils ('destringify'); use Bio::EnsEMBL::Hive::Utils ('destringify');
use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor; use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
......
...@@ -28,7 +28,8 @@ package Bio::EnsEMBL::Hive::AnalysisStats; ...@@ -28,7 +28,8 @@ package Bio::EnsEMBL::Hive::AnalysisStats;
use strict; use strict;
use Scalar::Util ('weaken'); use Scalar::Util ('weaken');
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()' use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Hive::Analysis; use Bio::EnsEMBL::Hive::Analysis;
......
...@@ -40,8 +40,6 @@ ...@@ -40,8 +40,6 @@
package Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor; package Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use strict; use strict;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor'); use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
......
...@@ -40,11 +40,11 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor; ...@@ -40,11 +40,11 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use strict; use strict;
use Bio::EnsEMBL::Utils::Argument; use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception; use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::Worker;
use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::AnalysisJob; use Bio::EnsEMBL::Hive::AnalysisJob;
use Bio::EnsEMBL::Hive::Utils 'stringify'; # import 'stringify()'
use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor'); use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
......
...@@ -40,9 +40,9 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor; ...@@ -40,9 +40,9 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor;
use strict; use strict;
use Bio::EnsEMBL::Hive::AnalysisStats;
use Bio::EnsEMBL::Utils::Argument; use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception; use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::AnalysisStats;
use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor'); use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
......
...@@ -36,7 +36,9 @@ Bio::EnsEMBL::Hive::DBSQL::DBAdaptor ...@@ -36,7 +36,9 @@ Bio::EnsEMBL::Hive::DBSQL::DBAdaptor
package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor; package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
use strict; use strict;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Hive::URLFactory; use Bio::EnsEMBL::Hive::URLFactory;
use Bio::EnsEMBL::Hive::DBSQL::DBConnection; use Bio::EnsEMBL::Hive::DBSQL::DBConnection;
......
...@@ -24,8 +24,8 @@ ...@@ -24,8 +24,8 @@
package Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor; package Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
use strict; use strict;
use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::DataflowRule; use Bio::EnsEMBL::Hive::DataflowRule;
use Bio::EnsEMBL::Hive::Utils ('stringify'); # import 'stringify()'
use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor'); use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
......
...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
=head1 DESCRIPTION =head1 DESCRIPTION
This module extends EnsEMBL Core's MetaContainer, adding some Hive-specific stuff. This module extends EnsEMBL Core's BaseMetaContainer, adding some Hive-specific stuff.
=head1 CONTACT =head1 CONTACT
...@@ -22,7 +22,7 @@ ...@@ -22,7 +22,7 @@
package Bio::EnsEMBL::Hive::DBSQL::MetaContainer; package Bio::EnsEMBL::Hive::DBSQL::MetaContainer;
use strict; use strict;
use Bio::EnsEMBL::Hive::Utils ('destringify'); # import both functions use Bio::EnsEMBL::Hive::Utils ('destringify');
use base ('Bio::EnsEMBL::DBSQL::BaseMetaContainer'); use base ('Bio::EnsEMBL::DBSQL::BaseMetaContainer');
......
...@@ -50,10 +50,11 @@ ...@@ -50,10 +50,11 @@
package Bio::EnsEMBL::Hive::DataflowRule; package Bio::EnsEMBL::Hive::DataflowRule;
use strict; use strict;
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()'
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Hive::Utils ('stringify'); # import 'stringify()' use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor; use Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
......
...@@ -22,7 +22,7 @@ package Bio::EnsEMBL::Hive::NakedTable; ...@@ -22,7 +22,7 @@ package Bio::EnsEMBL::Hive::NakedTable;
use strict; use strict;
use Scalar::Util ('weaken'); use Scalar::Util ('weaken');
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()' use Bio::EnsEMBL::Utils::Argument ('rearrange');
sub new { sub new {
my $class = shift @_; my $class = shift @_;
......
...@@ -48,8 +48,9 @@ package Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf; ...@@ -48,8 +48,9 @@ package Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
use strict; use strict;
use warnings; use warnings;
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()' use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Hive::Utils 'stringify'; # import 'stringify()'
use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor; use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor; use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use Bio::EnsEMBL::Hive::Analysis; use Bio::EnsEMBL::Hive::Analysis;
......
...@@ -86,9 +86,11 @@ package Bio::EnsEMBL::Hive::Process; ...@@ -86,9 +86,11 @@ package Bio::EnsEMBL::Hive::Process;
use strict; use strict;
use warnings; use warnings;
use Bio::EnsEMBL::Registry; use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Utils::Argument; use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw'); use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::DBSQL::DBConnection; use Bio::EnsEMBL::Hive::DBSQL::DBConnection;
use Bio::EnsEMBL::Hive::Utils ('stringify', 'go_figure_dbc'); use Bio::EnsEMBL::Hive::Utils ('stringify', 'go_figure_dbc');
use Bio::EnsEMBL::Hive::Utils::Stopwatch; use Bio::EnsEMBL::Hive::Utils::Stopwatch;
......
...@@ -63,10 +63,9 @@ use strict; ...@@ -63,10 +63,9 @@ use strict;
use POSIX; use POSIX;
use File::Path 'make_path'; use File::Path 'make_path';
use Bio::EnsEMBL::Utils::Argument; use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Hive::Utils ('destringify', 'dir_revhash'); # import 'destringify()' and 'dir_revhash()' use Bio::EnsEMBL::Hive::Utils ('destringify', 'dir_revhash'); # NB: needed by invisible code
use Bio::EnsEMBL::Hive::AnalysisJob; use Bio::EnsEMBL::Hive::AnalysisJob;
use Bio::EnsEMBL::Hive::Worker; use Bio::EnsEMBL::Hive::Worker;
......
...@@ -26,7 +26,8 @@ ...@@ -26,7 +26,8 @@
package Bio::EnsEMBL::Hive::ResourceClass; package Bio::EnsEMBL::Hive::ResourceClass;
use strict; use strict;
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()'
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
); );
......
...@@ -28,7 +28,7 @@ package Bio::EnsEMBL::Hive::ResourceDescription; ...@@ -28,7 +28,7 @@ package Bio::EnsEMBL::Hive::ResourceDescription;
use strict; use strict;
use Scalar::Util ('weaken'); use Scalar::Util ('weaken');
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()' use Bio::EnsEMBL::Utils::Argument ('rearrange');
sub new { sub new {
my $class = shift @_; my $class = shift @_;
......
...@@ -66,8 +66,7 @@ package Bio::EnsEMBL::Hive::Worker; ...@@ -66,8 +66,7 @@ package Bio::EnsEMBL::Hive::Worker;
use strict; use strict;
use POSIX; use POSIX;
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()' use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Hive::Analysis; use Bio::EnsEMBL::Hive::Analysis;
use Bio::EnsEMBL::Hive::AnalysisStats; use Bio::EnsEMBL::Hive::AnalysisStats;
......
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