Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
ensembl-gh-mirror
ensembl-hive
Commits
ba0f2590
Commit
ba0f2590
authored
May 23, 2013
by
Leo Gordon
Browse files
cosmetic: make it explicit that we are importing rearrange() and throw()
parent
5655fa32
Changes
19
Hide whitespace changes
Inline
Side-by-side
Showing
19 changed files
with
39 additions
and
32 deletions
+39
-32
modules/Bio/EnsEMBL/Hive/Accumulator.pm
modules/Bio/EnsEMBL/Hive/Accumulator.pm
+1
-1
modules/Bio/EnsEMBL/Hive/Analysis.pm
modules/Bio/EnsEMBL/Hive/Analysis.pm
+2
-1
modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
+3
-2
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
+2
-1
modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
+2
-1
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisDataAdaptor.pm
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisDataAdaptor.pm
+0
-2
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
+4
-4
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm
+2
-2
modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm
modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm
+3
-1
modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm
modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm
+1
-1
modules/Bio/EnsEMBL/Hive/DBSQL/MetaContainer.pm
modules/Bio/EnsEMBL/Hive/DBSQL/MetaContainer.pm
+2
-2
modules/Bio/EnsEMBL/Hive/DataflowRule.pm
modules/Bio/EnsEMBL/Hive/DataflowRule.pm
+4
-3
modules/Bio/EnsEMBL/Hive/NakedTable.pm
modules/Bio/EnsEMBL/Hive/NakedTable.pm
+1
-1
modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
+3
-2
modules/Bio/EnsEMBL/Hive/Process.pm
modules/Bio/EnsEMBL/Hive/Process.pm
+3
-1
modules/Bio/EnsEMBL/Hive/Queen.pm
modules/Bio/EnsEMBL/Hive/Queen.pm
+2
-3
modules/Bio/EnsEMBL/Hive/ResourceClass.pm
modules/Bio/EnsEMBL/Hive/ResourceClass.pm
+2
-1
modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
+1
-1
modules/Bio/EnsEMBL/Hive/Worker.pm
modules/Bio/EnsEMBL/Hive/Worker.pm
+1
-2
No files found.
modules/Bio/EnsEMBL/Hive/Accumulator.pm
View file @
ba0f2590
...
...
@@ -22,7 +22,7 @@ package Bio::EnsEMBL::Hive::Accumulator;
use
strict
;
use
Scalar::
Util
('
weaken
');
use
Bio::EnsEMBL::Utils::
Argument
;
# import
'rearrange
()'
use
Bio::EnsEMBL::Utils::
Argument
(
'
rearrange
');
sub
new
{
my
$class
=
shift
@_
;
...
...
modules/Bio/EnsEMBL/Hive/Analysis.pm
View file @
ba0f2590
...
...
@@ -24,7 +24,8 @@
package
Bio::EnsEMBL::Hive::
Analysis
;
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
);
...
...
modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
View file @
ba0f2590
...
...
@@ -44,10 +44,11 @@ package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
use
strict
;
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::
Extensions
;
use
Bio::EnsEMBL::Utils::
Argument
;
use
Bio::EnsEMBL::Utils::
Exception
;
=head2 new
...
...
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
View file @
ba0f2590
...
...
@@ -27,7 +27,8 @@
package
Bio::EnsEMBL::Hive::
AnalysisJob
;
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::DBSQL::
AnalysisJobAdaptor
;
...
...
modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
View file @
ba0f2590
...
...
@@ -28,7 +28,8 @@ package Bio::EnsEMBL::Hive::AnalysisStats;
use
strict
;
use
Scalar::
Util
('
weaken
');
use
Bio::EnsEMBL::Utils::
Argument
;
# import 'rearrange()'
use
Bio::EnsEMBL::Utils::
Argument
('
rearrange
');
use
Bio::EnsEMBL::Hive::
Analysis
;
...
...
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisDataAdaptor.pm
View file @
ba0f2590
...
...
@@ -40,8 +40,6 @@
package
Bio::EnsEMBL::Hive::DBSQL::
AnalysisDataAdaptor
;
use
strict
;
use
Bio::EnsEMBL::Utils::
Argument
qw(rearrange)
;
use
Bio::EnsEMBL::Utils::
Exception
qw(throw)
;
use
base
('
Bio::EnsEMBL::DBSQL::BaseAdaptor
');
...
...
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
View file @
ba0f2590
...
...
@@ -40,11 +40,11 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use
strict
;
use
Bio::EnsEMBL::Utils::
Argument
;
use
Bio::EnsEMBL::Utils::
Exception
;
use
Bio::EnsEMBL::Hive::
Worker
;
use
Bio::EnsEMBL::Utils::
Argument
('
rearrange
');
use
Bio::EnsEMBL::Utils::
Exception
('
throw
');
use
Bio::EnsEMBL::Hive::
Utils
('
stringify
');
use
Bio::EnsEMBL::Hive::
AnalysisJob
;
use
Bio::EnsEMBL::Hive::
Utils
'
stringify
';
# import 'stringify()'
use
base
('
Bio::EnsEMBL::DBSQL::BaseAdaptor
');
...
...
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm
View file @
ba0f2590
...
...
@@ -40,9 +40,9 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor;
use
strict
;
use
Bio::EnsEMBL::Hive::
AnalysisStats
;
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
');
...
...
modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm
View file @
ba0f2590
...
...
@@ -36,7 +36,9 @@ Bio::EnsEMBL::Hive::DBSQL::DBAdaptor
package
Bio::EnsEMBL::Hive::DBSQL::
DBAdaptor
;
use
strict
;
use
Bio::EnsEMBL::Utils::
Argument
;
use
Bio::EnsEMBL::Utils::
Argument
('
rearrange
');
use
Bio::EnsEMBL::Hive::
URLFactory
;
use
Bio::EnsEMBL::Hive::DBSQL::
DBConnection
;
...
...
modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm
View file @
ba0f2590
...
...
@@ -24,8 +24,8 @@
package
Bio::EnsEMBL::Hive::DBSQL::
DataflowRuleAdaptor
;
use
strict
;
use
Bio::EnsEMBL::Hive::
Utils
('
stringify
');
use
Bio::EnsEMBL::Hive::
DataflowRule
;
use
Bio::EnsEMBL::Hive::
Utils
('
stringify
');
# import 'stringify()'
use
base
('
Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor
');
...
...
modules/Bio/EnsEMBL/Hive/DBSQL/MetaContainer.pm
View file @
ba0f2590
...
...
@@ -10,7 +10,7 @@
=head1 DESCRIPTION
This module extends EnsEMBL Core's MetaContainer, adding some Hive-specific stuff.
This module extends EnsEMBL Core's
Base
MetaContainer, adding some Hive-specific stuff.
=head1 CONTACT
...
...
@@ -22,7 +22,7 @@
package
Bio::EnsEMBL::Hive::DBSQL::
MetaContainer
;
use
strict
;
use
Bio::EnsEMBL::Hive::
Utils
('
destringify
');
# import both functions
use
Bio::EnsEMBL::Hive::
Utils
('
destringify
');
use
base
('
Bio::EnsEMBL::DBSQL::BaseMetaContainer
');
...
...
modules/Bio/EnsEMBL/Hive/DataflowRule.pm
View file @
ba0f2590
...
...
@@ -50,10 +50,11 @@
package
Bio::EnsEMBL::Hive::
DataflowRule
;
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
base
(
'
Bio::EnsEMBL::Storable
',
# inherit dbID(), adaptor() and new() methods
...
...
modules/Bio/EnsEMBL/Hive/NakedTable.pm
View file @
ba0f2590
...
...
@@ -22,7 +22,7 @@ package Bio::EnsEMBL::Hive::NakedTable;
use
strict
;
use
Scalar::
Util
('
weaken
');
use
Bio::EnsEMBL::Utils::
Argument
;
# import
'rearrange
()'
use
Bio::EnsEMBL::Utils::
Argument
(
'
rearrange
');
sub
new
{
my
$class
=
shift
@_
;
...
...
modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
View file @
ba0f2590
...
...
@@ -48,8 +48,9 @@ package Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
use
strict
;
use
warnings
;
use
Bio::EnsEMBL::Utils::
Argument
;
# import 'rearrange()'
use
Bio::EnsEMBL::Hive::
Utils
'
stringify
';
# import 'stringify()'
use
Bio::EnsEMBL::Utils::
Argument
('
rearrange
');
use
Bio::EnsEMBL::Hive::
Utils
('
stringify
');
use
Bio::EnsEMBL::Hive::DBSQL::
DBAdaptor
;
use
Bio::EnsEMBL::Hive::DBSQL::
AnalysisJobAdaptor
;
use
Bio::EnsEMBL::Hive::
Analysis
;
...
...
modules/Bio/EnsEMBL/Hive/Process.pm
View file @
ba0f2590
...
...
@@ -86,9 +86,11 @@ package Bio::EnsEMBL::Hive::Process;
use
strict
;
use
warnings
;
use
Bio::EnsEMBL::
Registry
;
use
Bio::EnsEMBL::Utils::
Argument
;
use
Bio::EnsEMBL::Utils::
Argument
('
rearrange
')
;
use
Bio::EnsEMBL::Utils::
Exception
('
throw
');
use
Bio::EnsEMBL::Hive::DBSQL::
DBConnection
;
use
Bio::EnsEMBL::Hive::
Utils
('
stringify
',
'
go_figure_dbc
');
use
Bio::EnsEMBL::Hive::Utils::
Stopwatch
;
...
...
modules/Bio/EnsEMBL/Hive/Queen.pm
View file @
ba0f2590
...
...
@@ -63,10 +63,9 @@ use strict;
use
POSIX
;
use
File::
Path
'
make_path
';
use
Bio::EnsEMBL::Utils::
Argument
;
use
Bio::EnsEMBL::Utils::
Exception
;
use
Bio::EnsEMBL::Utils::
Argument
('
rearrange
');
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::
Worker
;
...
...
modules/Bio/EnsEMBL/Hive/ResourceClass.pm
View file @
ba0f2590
...
...
@@ -26,7 +26,8 @@
package
Bio::EnsEMBL::Hive::
ResourceClass
;
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
);
...
...
modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
View file @
ba0f2590
...
...
@@ -28,7 +28,7 @@ package Bio::EnsEMBL::Hive::ResourceDescription;
use
strict
;
use
Scalar::
Util
('
weaken
');
use
Bio::EnsEMBL::Utils::
Argument
;
# import
'rearrange
()'
use
Bio::EnsEMBL::Utils::
Argument
(
'
rearrange
');
sub
new
{
my
$class
=
shift
@_
;
...
...
modules/Bio/EnsEMBL/Hive/Worker.pm
View file @
ba0f2590
...
...
@@ -66,8 +66,7 @@ package Bio::EnsEMBL::Hive::Worker;
use
strict
;
use
POSIX
;
use
Bio::EnsEMBL::Utils::
Argument
;
# import 'rearrange()'
use
Bio::EnsEMBL::Utils::
Exception
;
use
Bio::EnsEMBL::Utils::
Argument
('
rearrange
');
use
Bio::EnsEMBL::Hive::
Analysis
;
use
Bio::EnsEMBL::Hive::
AnalysisStats
;
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment