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  • 4 commits
  • 18 files changed
  • 0 commit comments
  • 1 contributor
Commits on May 30, 2012
Ray Miller Update for new input field names 57db08a
Commits on Aug 01, 2012
Ray Miller Address Perl::Criitc issues 037e6a8
Ray Miller Implement CleanReportCache task 90a0ba6
Ray Miller Initial release. 1087587
View
3 .gitignore
@@ -1,3 +0,0 @@
-.build
-.LIMS2-Tasks-*
-*~
View
3 Changes
@@ -0,0 +1,3 @@
+0.001 2012-08-01 11:43:12 Europe/London
+
+ Initial release.
View
379 LICENSE
@@ -0,0 +1,379 @@
+This software is copyright (c) 2012 by Genome Research Ltd.
+
+This is free software; you can redistribute it and/or modify it under
+the same terms as the Perl 5 programming language system itself.
+
+Terms of the Perl programming language system itself
+
+a) the GNU General Public License as published by the Free
+ Software Foundation; either version 1, or (at your option) any
+ later version, or
+b) the "Artistic License"
+
+--- The GNU General Public License, Version 1, February 1989 ---
+
+This software is Copyright (c) 2012 by Genome Research Ltd.
+
+This is free software, licensed under:
+
+ The GNU General Public License, Version 1, February 1989
+
+ GNU GENERAL PUBLIC LICENSE
+ Version 1, February 1989
+
+ Copyright (C) 1989 Free Software Foundation, Inc.
+ 51 Franklin St, Suite 500, Boston, MA 02110-1335 USA
+
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The license agreements of most software companies try to keep users
+at the mercy of those companies. By contrast, our General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. The
+General Public License applies to the Free Software Foundation's
+software and to any other program whose authors commit to using it.
+You can use it for your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Specifically, the General Public License is designed to make
+sure that you have the freedom to give away or sell copies of free
+software, that you receive source code or can get it if you want it,
+that you can change the software or use pieces of it in new free
+programs; and that you know you can do these things.
+
+ To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+ For example, if you distribute copies of a such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have. You must make sure that they, too, receive or can get the
+source code. And you must tell them their rights.
+
+ We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+ Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software. If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ GNU GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License Agreement applies to any program or other work which
+contains a notice placed by the copyright holder saying it may be
+distributed under the terms of this General Public License. The
+"Program", below, refers to any such program or work, and a "work based
+on the Program" means either the Program or any work containing the
+Program or a portion of it, either verbatim or with modifications. Each
+licensee is addressed as "you".
+
+ 1. You may copy and distribute verbatim copies of the Program's source
+code as you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this
+General Public License and to the absence of any warranty; and give any
+other recipients of the Program a copy of this General Public License
+along with the Program. You may charge a fee for the physical act of
+transferring a copy.
+
+ 2. You may modify your copy or copies of the Program or any portion of
+it, and copy and distribute such modifications under the terms of Paragraph
+1 above, provided that you also do the following:
+
+ a) cause the modified files to carry prominent notices stating that
+ you changed the files and the date of any change; and
+
+ b) cause the whole of any work that you distribute or publish, that
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+ third parties, at your option).
+
+ c) If the modified program normally reads commands interactively when
+ run, you must cause it, when started running for such interactive use
+ in the simplest and most usual way, to print or display an
+ announcement including an appropriate copyright notice and a notice
+ that there is no warranty (or else, saying that you provide a
+ warranty) and that users may redistribute the program under these
+ conditions, and telling the user how to view a copy of this General
+ Public License.
+
+ d) You may charge a fee for the physical act of transferring a
+ copy, and you may at your option offer warranty protection in
+ exchange for a fee.
+
+Mere aggregation of another independent work with the Program (or its
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+the other work under the scope of these terms.
+
+ 3. You may copy and distribute the Program (or a portion or derivative of
+it, under Paragraph 2) in object code or executable form under the terms of
+Paragraphs 1 and 2 above provided that you also do one of the following:
+
+ a) accompany it with the complete corresponding machine-readable
+ source code, which must be distributed under the terms of
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+
+ b) accompany it with a written offer, valid for at least three
+ years, to give any third party free (except for a nominal charge
+ for the cost of distribution) a complete machine-readable copy of the
+ corresponding source code, to be distributed under the terms of
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+
+ c) accompany it with the information you received as to where the
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+ allowed only for noncommercial distribution and only if you
+ received the program in object code or executable form alone.)
+
+Source code for a work means the preferred form of the work for making
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+
+ 4. You may not copy, modify, sublicense, distribute or transfer the
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+Any attempt otherwise to copy, modify, sublicense, distribute or transfer
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+the Program under this License. However, parties who have received
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+
+ 5. By copying, distributing or modifying the Program (or any work based
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+
+ 6. Each time you redistribute the Program (or any work based on the
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+
+ 7. The Free Software Foundation may publish revised and/or new versions
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+
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+either of that version or of any later version published by the Free
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+
+ 8. If you wish to incorporate parts of the Program into other free
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+
+ NO WARRANTY
+
+ 9. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+ 10. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+
+ Appendix: How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to humanity, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these
+terms.
+
+ To do so, attach the following notices to the program. It is safest to
+attach them to the start of each source file to most effectively convey
+the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) 19yy <name of author>
+
+ 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
+ the Free Software Foundation; either version 1, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) 19xx name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the
+appropriate parts of the General Public License. Of course, the
+commands you use may be called something other than `show w' and `show
+c'; they could even be mouse-clicks or menu items--whatever suits your
+program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the
+ program `Gnomovision' (a program to direct compilers to make passes
+ at assemblers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+That's all there is to it!
+
+
+--- The Artistic License 1.0 ---
+
+This software is Copyright (c) 2012 by Genome Research Ltd.
+
+This is free software, licensed under:
+
+ The Artistic License 1.0
+
+The Artistic License
+
+Preamble
+
+The intent of this document is to state the conditions under which a Package
+may be copied, such that the Copyright Holder maintains some semblance of
+artistic control over the development of the package, while giving the users of
+the package the right to use and distribute the Package in a more-or-less
+customary fashion, plus the right to make reasonable modifications.
+
+Definitions:
+
+ - "Package" refers to the collection of files distributed by the Copyright
+ Holder, and derivatives of that collection of files created through
+ textual modification.
+ - "Standard Version" refers to such a Package if it has not been modified,
+ or has been modified in accordance with the wishes of the Copyright
+ Holder.
+ - "Copyright Holder" is whoever is named in the copyright or copyrights for
+ the package.
+ - "You" is you, if you're thinking about copying or distributing this Package.
+ - "Reasonable copying fee" is whatever you can justify on the basis of media
+ cost, duplication charges, time of people involved, and so on. (You will
+ not be required to justify it to the Copyright Holder, but only to the
+ computing community at large as a market that must bear the fee.)
+ - "Freely Available" means that no fee is charged for the item itself, though
+ there may be fees involved in handling the item. It also means that
+ recipients of the item may redistribute it under the same conditions they
+ received it.
+
+1. You may make and give away verbatim copies of the source form of the
+Standard Version of this Package without restriction, provided that you
+duplicate all of the original copyright notices and associated disclaimers.
+
+2. You may apply bug fixes, portability fixes and other modifications derived
+from the Public Domain or from the Copyright Holder. A Package modified in such
+a way shall still be considered the Standard Version.
+
+3. You may otherwise modify your copy of this Package in any way, provided that
+you insert a prominent notice in each changed file stating how and when you
+changed that file, and provided that you do at least ONE of the following:
+
+ a) place your modifications in the Public Domain or otherwise make them
+ Freely Available, such as by posting said modifications to Usenet or an
+ equivalent medium, or placing the modifications on a major archive site
+ such as ftp.uu.net, or by allowing the Copyright Holder to include your
+ modifications in the Standard Version of the Package.
+
+ b) use the modified Package only within your corporation or organization.
+
+ c) rename any non-standard executables so the names do not conflict with
+ standard executables, which must also be provided, and provide a separate
+ manual page for each non-standard executable that clearly documents how it
+ differs from the Standard Version.
+
+ d) make other distribution arrangements with the Copyright Holder.
+
+4. You may distribute the programs of this Package in object code or executable
+form, provided that you do at least ONE of the following:
+
+ a) distribute a Standard Version of the executables and library files,
+ together with instructions (in the manual page or equivalent) on where to
+ get the Standard Version.
+
+ b) accompany the distribution with the machine-readable source of the Package
+ with your modifications.
+
+ c) accompany any non-standard executables with their corresponding Standard
+ Version executables, giving the non-standard executables non-standard
+ names, and clearly documenting the differences in manual pages (or
+ equivalent), together with instructions on where to get the Standard
+ Version.
+
+ d) make other distribution arrangements with the Copyright Holder.
+
+5. You may charge a reasonable copying fee for any distribution of this
+Package. You may charge any fee you choose for support of this Package. You
+may not charge a fee for this Package itself. However, you may distribute this
+Package in aggregate with other (possibly commercial) programs as part of a
+larger (possibly commercial) software distribution provided that you do not
+advertise this Package as a product of your own.
+
+6. The scripts and library files supplied as input to or produced as output
+from the programs of this Package do not automatically fall under the copyright
+of this Package, but belong to whomever generated them, and may be sold
+commercially, and may be aggregated with this Package.
+
+7. C or perl subroutines supplied by you and linked into this Package shall not
+be considered part of this Package.
+
+8. The name of the Copyright Holder may not be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
+MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+The End
+
View
17 MANIFEST
@@ -0,0 +1,17 @@
+Changes
+LICENSE
+MANIFEST
+META.yml
+Makefile.PL
+README
+bin/lims2-task
+lib/LIMS2/Task.pm
+lib/LIMS2/Task/General/CleanReportCache.pm
+lib/LIMS2/Task/YAMLDataLoader.pm
+lib/LIMS2/Task/YAMLDataLoader/LoadBacs.pm
+lib/LIMS2/Task/YAMLDataLoader/LoadDesigns.pm
+lib/LIMS2/Task/YAMLDataLoader/LoadUsers.pm
+lib/LIMS2/Tasks.pm
+t/00-compile.t
+t/author-critic.t
+t/release-no-smart-comments.t
View
35 META.yml
@@ -0,0 +1,35 @@
+---
+abstract: 'Script and task framework for LIMS2'
+author:
+ - 'Ray Miller <rm7@sanger.ac.uk>'
+build_requires:
+ English: 0
+ File::Find: 0
+ File::Temp: 0
+ Test::More: 0.88
+configure_requires:
+ ExtUtils::MakeMaker: 6.30
+dynamic_config: 0
+generated_by: 'Dist::Zilla version 4.300014, CPAN::Meta::Converter version 2.120921'
+license: perl
+meta-spec:
+ url: http://module-build.sourceforge.net/META-spec-v1.4.html
+ version: 1.4
+name: LIMS2-Tasks
+requires:
+ LIMS2::Model: 0
+ LIMS2::Model::DBConnect: 0
+ LIMS2::Report: 0
+ LIMS2::Util::EnsEMBL: 0
+ LIMS2::Util::YAMLIterator: 0
+ List::MoreUtils: 0
+ Log::Log4perl: 0
+ Moose: 0
+ MooseX::App::Cmd: 0
+ MooseX::App::Cmd::Command: 0
+ MooseX::Log::Log4perl: 0
+ Try::Tiny: 0
+ namespace::autoclean: 0
+ strict: 0
+ warnings: 0
+version: 0.001
View
72 Makefile.PL
@@ -0,0 +1,72 @@
+
+use strict;
+use warnings;
+
+
+
+use ExtUtils::MakeMaker 6.30;
+
+
+
+my %WriteMakefileArgs = (
+ "ABSTRACT" => "Script and task framework for LIMS2",
+ "AUTHOR" => "Ray Miller <rm7\@sanger.ac.uk>",
+ "BUILD_REQUIRES" => {
+ "English" => 0,
+ "File::Find" => 0,
+ "File::Temp" => 0,
+ "Test::More" => "0.88"
+ },
+ "CONFIGURE_REQUIRES" => {
+ "ExtUtils::MakeMaker" => "6.30"
+ },
+ "DISTNAME" => "LIMS2-Tasks",
+ "EXE_FILES" => [
+ "bin/lims2-task"
+ ],
+ "LICENSE" => "perl",
+ "NAME" => "LIMS2::Tasks",
+ "PREREQ_PM" => {
+ "LIMS2::Model" => 0,
+ "LIMS2::Model::DBConnect" => 0,
+ "LIMS2::Report" => 0,
+ "LIMS2::Util::EnsEMBL" => 0,
+ "LIMS2::Util::YAMLIterator" => 0,
+ "List::MoreUtils" => 0,
+ "Log::Log4perl" => 0,
+ "Moose" => 0,
+ "MooseX::App::Cmd" => 0,
+ "MooseX::App::Cmd::Command" => 0,
+ "MooseX::Log::Log4perl" => 0,
+ "Try::Tiny" => 0,
+ "namespace::autoclean" => 0,
+ "strict" => 0,
+ "warnings" => 0
+ },
+ "VERSION" => "0.001",
+ "test" => {
+ "TESTS" => "t/*.t"
+ }
+);
+
+
+unless ( eval { ExtUtils::MakeMaker->VERSION(6.56) } ) {
+ my $br = delete $WriteMakefileArgs{BUILD_REQUIRES};
+ my $pp = $WriteMakefileArgs{PREREQ_PM};
+ for my $mod ( keys %$br ) {
+ if ( exists $pp->{$mod} ) {
+ $pp->{$mod} = $br->{$mod} if $br->{$mod} > $pp->{$mod};
+ }
+ else {
+ $pp->{$mod} = $br->{$mod};
+ }
+ }
+}
+
+delete $WriteMakefileArgs{CONFIGURE_REQUIRES}
+ unless eval { ExtUtils::MakeMaker->VERSION(6.52) };
+
+WriteMakefile(%WriteMakefileArgs);
+
+
+
View
13 README
@@ -0,0 +1,13 @@
+
+
+This archive contains the distribution LIMS2-Tasks,
+version 0.001:
+
+ Script and task framework for LIMS2
+
+This software is copyright (c) 2012 by Genome Research Ltd.
+
+This is free software; you can redistribute it and/or modify it under
+the same terms as the Perl 5 programming language system itself.
+
+
View
8 dist.ini
@@ -1,8 +0,0 @@
-name = LIMS2-Tasks
-abstract = Script and task framework for LIMS2
-author = Ray Miller <rm7@sanger.ac.uk>
-license = Perl_5
-copyright_holder = Genome Research Ltd
-copyright_year = 2012
-
-[@Author::HTGT]
View
11 lib/LIMS2/Task.pm
@@ -1,4 +1,10 @@
package LIMS2::Task;
+## no critic(RequireUseStrict,RequireUseWarnings)
+{
+ $LIMS2::Task::VERSION = '0.001';
+}
+## use critic
+
use strict;
use warnings FATAL => 'all';
@@ -62,7 +68,7 @@ has schema => (
sub _build_schema {
my $self = shift;
- LIMS2::Model::DBConnect->connect( 'LIMS2_DB', 'tasks' );
+ return LIMS2::Model::DBConnect->connect( 'LIMS2_DB', 'tasks' );
}
has model => (
@@ -75,7 +81,7 @@ has model => (
sub _build_model {
my $self = shift;
require LIMS2::Model;
- LIMS2::Model->new( schema => $self->schema );
+ return LIMS2::Model->new( schema => $self->schema );
}
has ensembl_util => (
@@ -101,6 +107,7 @@ sub BUILD {
: $WARN;
Log::Log4perl->easy_init( { level => $log_level, layout => $self->log_layout } );
+ return;
}
override command_names => sub {
View
36 lib/LIMS2/Task/General/CleanReportCache.pm
@@ -0,0 +1,36 @@
+package LIMS2::Task::General::CleanReportCache;
+## no critic(RequireUseStrict,RequireUseWarnings)
+{
+ $LIMS2::Task::General::CleanReportCache::VERSION = '0.001';
+}
+## use critic
+
+
+use strict;
+use warnings FATAL => 'all';
+
+use Moose;
+use LIMS2::Report;
+use namespace::autoclean;
+
+extends 'LIMS2::Task';
+
+override abstract => sub {
+ 'Delete stale entries from the report cache';
+};
+
+sub execute {
+ my ( $self, $opts, $args ) = @_;
+
+ my $verbose = $self->trace || $self->debug || $self->verbose;
+
+ LIMS2::Report::clean_cache( $self->model, $verbose );
+
+ return;
+}
+
+__PACKAGE__->meta->make_immutable;
+
+1;
+
+__END__
View
16 lib/LIMS2/Task/YAMLDataLoader.pm
@@ -1,4 +1,10 @@
package LIMS2::Task::YAMLDataLoader;
+## no critic(RequireUseStrict,RequireUseWarnings)
+{
+ $LIMS2::Task::YAMLDataLoader::VERSION = '0.001';
+}
+## use critic
+
use strict;
use warnings FATAL => 'all';
@@ -52,7 +58,7 @@ sub execute {
$self->log->info( "Running " . $self->abstract );
my ( $total_seen, $total_skipped, $total_err ) = (0,0,0);
-
+
for my $input_file ( @{$args} ) {
my ( $file_seen, $file_skipped, $file_err ) = $self->load_data_from_file( $input_file );
$total_seen += $file_seen;
@@ -61,11 +67,13 @@ sub execute {
}
$self->log->info( "Processed $total_seen records (skipped $total_skipped, failed $total_err)" );
+
+ return;
}
sub load_data_from_file {
my ( $self, $input_file ) = @_;
-
+
$self->log->info( "Loading data from $input_file" );
my ($file_seen, $file_skipped, $file_err) = (0,0,0);
my $it = iyaml( $input_file );
@@ -73,11 +81,11 @@ sub load_data_from_file {
$file_seen++;
if ( ! $self->wanted( $datum ) ) {
$file_skipped++;
- next;
+ next;
}
try {
$self->model->txn_do(
- sub {
+ sub {
$self->create( $datum );
unless ( $self->commit ) {
$self->model->txn_rollback;
View
6 lib/LIMS2/Task/YAMLDataLoader/LoadBacs.pm
@@ -1,4 +1,10 @@
package LIMS2::Task::YAMLDataLoader::LoadBacs;
+## no critic(RequireUseStrict,RequireUseWarnings)
+{
+ $LIMS2::Task::YAMLDataLoader::LoadBacs::VERSION = '0.001';
+}
+## use critic
+
use strict;
use warnings FATAL => 'all';
View
14 lib/LIMS2/Task/YAMLDataLoader/LoadDesigns.pm
@@ -1,4 +1,10 @@
package LIMS2::Task::YAMLDataLoader::LoadDesigns;
+## no critic(RequireUseStrict,RequireUseWarnings)
+{
+ $LIMS2::Task::YAMLDataLoader::LoadDesigns::VERSION = '0.001';
+}
+## use critic
+
use strict;
use warnings FATAL => 'all';
@@ -23,20 +29,20 @@ override create => sub {
override record_key => sub {
my ( $self, $datum ) = @_;
- return $datum->{design_id} || '<undef>';
+ return $datum->{id} || '<undef>';
};
override wanted => sub {
my ( $self, $datum ) = @_;
unless ( defined $datum->{phase} ) {
- $self->log->warn( "Skipping design $datum->{design_id} - no phase" );
+ $self->log->warn( "Skipping design $datum->{id} - no phase" );
return 0;
}
for my $primer ( @{ $datum->{genotyping_primers} || [] } ) {
- unless ( defined $primer->{genotyping_primer_seq} ) {
- $self->log->warn( "Skipping design $datum->{design_id} - no seq for primer $primer->{genotyping_primer_type}" );
+ unless ( defined $primer->{seq} ) {
+ $self->log->warn( "Skipping design $datum->{id} - no seq for primer $primer->{type}" );
return 0;
}
}
View
6 lib/LIMS2/Task/YAMLDataLoader/LoadUsers.pm
@@ -1,4 +1,10 @@
package LIMS2::Task::YAMLDataLoader::LoadUsers;
+## no critic(RequireUseStrict,RequireUseWarnings)
+{
+ $LIMS2::Task::YAMLDataLoader::LoadUsers::VERSION = '0.001';
+}
+## use critic
+
use strict;
use warnings FATAL => 'all';
View
10 lib/LIMS2/Tasks.pm
@@ -1,4 +1,10 @@
package LIMS2::Tasks;
+## no critic(RequireUseStrict,RequireUseWarnings)
+{
+ $LIMS2::Tasks::VERSION = '0.001';
+}
+## use critic
+
use strict;
use warnings FATAL => 'all';
@@ -8,7 +14,9 @@ use namespace::autoclean;
extends 'MooseX::App::Cmd';
-use constant plugin_search_path => [ 'LIMS2::Task::General', 'LIMS2::Task::YAMLDataLoader' ];
+sub plugin_search_path {
+ return [ 'LIMS2::Task::General', 'LIMS2::Task::YAMLDataLoader' ];
+}
__PACKAGE__->meta->make_immutable;
View
73 t/00-compile.t
@@ -0,0 +1,73 @@
+#!perl
+
+use strict;
+use warnings;
+
+use Test::More;
+
+
+
+use File::Find;
+use File::Temp qw{ tempdir };
+
+my @modules;
+find(
+ sub {
+ return if $File::Find::name !~ /\.pm\z/;
+ my $found = $File::Find::name;
+ $found =~ s{^lib/}{};
+ $found =~ s{[/\\]}{::}g;
+ $found =~ s/\.pm$//;
+ # nothing to skip
+ push @modules, $found;
+ },
+ 'lib',
+);
+
+sub _find_scripts {
+ my $dir = shift @_;
+
+ my @found_scripts = ();
+ find(
+ sub {
+ return unless -f;
+ my $found = $File::Find::name;
+ # nothing to skip
+ open my $FH, '<', $_ or do {
+ note( "Unable to open $found in ( $! ), skipping" );
+ return;
+ };
+ my $shebang = <$FH>;
+ return unless $shebang =~ /^#!.*?\bperl\b\s*$/;
+ push @found_scripts, $found;
+ },
+ $dir,
+ );
+
+ return @found_scripts;
+}
+
+my @scripts;
+do { push @scripts, _find_scripts($_) if -d $_ }
+ for qw{ bin script scripts };
+
+my $plan = scalar(@modules) + scalar(@scripts);
+$plan ? (plan tests => $plan) : (plan skip_all => "no tests to run");
+
+{
+ # fake home for cpan-testers
+ # no fake requested ## local $ENV{HOME} = tempdir( CLEANUP => 1 );
+
+ like( qx{ $^X -Ilib -e "require $_; print '$_ ok'" }, qr/^\s*$_ ok/s, "$_ loaded ok" )
+ for sort @modules;
+
+ SKIP: {
+ eval "use Test::Script 1.05; 1;";
+ skip "Test::Script needed to test script compilation", scalar(@scripts) if $@;
+ foreach my $file ( @scripts ) {
+ my $script = $file;
+ $script =~ s!.*/!!;
+ script_compiles( $file, "$script script compiles" );
+ }
+ }
+}
View
20 t/author-critic.t
@@ -0,0 +1,20 @@
+#!perl
+
+BEGIN {
+ unless ($ENV{AUTHOR_TESTING}) {
+ require Test::More;
+ Test::More::plan(skip_all => 'these tests are for testing by the author');
+ }
+}
+
+
+use strict;
+use warnings;
+
+use Test::More;
+use English qw(-no_match_vars);
+
+eval "use Test::Perl::Critic";
+plan skip_all => 'Test::Perl::Critic required to criticise code' if $@;
+Test::Perl::Critic->import( -profile => "/opt/t87/global/conf/perlcritic.rc" ) if -e "/opt/t87/global/conf/perlcritic.rc";
+all_critic_ok();
View
22 t/release-no-smart-comments.t
@@ -0,0 +1,22 @@
+#!/usr/bin/env perl
+
+BEGIN {
+ unless ($ENV{RELEASE_TESTING}) {
+ require Test::More;
+ Test::More::plan(skip_all => 'these tests are for release candidate testing');
+ }
+}
+
+
+use strict;
+use warnings;
+
+use Test::More 0.88;
+
+eval "use Test::NoSmartComments";
+plan skip_all => 'Test::NoSmartComments required for checking comment IQ'
+ if $@;
+
+no_smart_comments_in_all();
+
+done_testing();

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