Added DesignVectors report

htgt · Feb 28, 2013 · 430b758 · 430b758
2 parents 3854348 + 2d8df83
commit 430b758
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diff --git a/Changes b/Changes
@@ -1,3 +1,12 @@
+0.054     2013-02-28 10:45:42 Europe/London
+
+	Added DesignVectors report
+
+0.053     2013-02-26 16:13:34 Europe/London
+
+    Copy Plate backend added
+    Final Pick process and plate type added
+
 0.052     2013-02-21 09:52:15 Europe/London
 
 	GenesToElectroporate report now generated from summaries table

diff --git a/MANIFEST b/MANIFEST
@@ -130,9 +130,11 @@ lib/LIMS2/Model/Util/WellName.pm
 lib/LIMS2/Report.pm
 lib/LIMS2/Report/DNAPlate.pm
 lib/LIMS2/Report/DesignPlate.pm
+lib/LIMS2/Report/DesignVectors.pm
 lib/LIMS2/Report/EPPlate.pm
 lib/LIMS2/Report/ElectroporationProductionSummary.pm
 lib/LIMS2/Report/FPPlate.pm
+lib/LIMS2/Report/FinalPickVectorPlate.pm
 lib/LIMS2/Report/FinalVectorPlate.pm
 lib/LIMS2/Report/FirstElectroporationProductionDetail.pm
 lib/LIMS2/Report/GenesToElectroporate.pm
@@ -173,6 +175,7 @@ lib/LIMS2/WebApp/Controller/User/BrowseDesigns.pm
 lib/LIMS2/WebApp/Controller/User/BrowsePlates.pm
 lib/LIMS2/WebApp/Controller/User/BrowseTemplates.pm
 lib/LIMS2/WebApp/Controller/User/Graph.pm
+lib/LIMS2/WebApp/Controller/User/PlateCopy.pm
 lib/LIMS2/WebApp/Controller/User/PlateEdit.pm
 lib/LIMS2/WebApp/Controller/User/PlateUpload.pm
 lib/LIMS2/WebApp/Controller/User/QC.pm
@@ -190,6 +193,7 @@ root/favicon.ico
 root/lib/colony_count_upload_help.tt
 root/lib/navigation.tt
 root/lib/pagination.tt
+root/lib/plate_copy_help.tt
 root/lib/plate_upload_help.tt
 root/lib/process_specific_fields.tt
 root/lib/recombinase_upload_help.tt
@@ -211,6 +215,8 @@ root/site/user/browsetemplates/view.tt
 root/site/user/error.tt
 root/site/user/graph/index.tt
 root/site/user/index.tt
+root/site/user/platecopy/plate_copy_wait.tt
+root/site/user/platecopy/plate_from_copy.tt
 root/site/user/plateupload/plate_upload_step1.tt
 root/site/user/plateupload/plate_upload_step2.tt
 root/site/user/qc/create_plates.tt
@@ -226,6 +232,7 @@ root/site/user/recombinaseupload/recombinase_upload.tt
 root/site/user/report/await_report.tt
 root/site/user/report/gene_report.tt
 root/site/user/report/select_sponsor.tt
+root/site/user/report/select_vector_params.tt
 root/site/user/report/simple_table.tt
 root/site/user/userpreferences/change_password.tt
 root/site/user/welldata/dna_status_update.tt
@@ -1721,6 +1728,7 @@ t/data/csv_upload_linux.csv
 t/data/csv_upload_mac.csv
 t/data/csv_upload_win.csv
 t/data/dna_prep_process.yaml
+t/data/final_pick_process.yaml
 t/data/first_electroporation.yaml
 t/data/freeze_process.yaml
 t/data/int_recom_process.yaml
@@ -1739,4 +1747,3 @@ t/data/well_850_user_params.yaml
 t/fixtures/00-clean-db.sql
 t/fixtures/10-load-fixture-data.sql
 t/release-no-smart-comments.t
-test.pl~
diff --git a/META.yml b/META.yml
@@ -124,4 +124,4 @@ requires:
   strict: 0
   utf8: 0
   warnings: 0
-version: 0.052
+version: 0.054
diff --git a/README b/README
@@ -1,7 +1,7 @@
 
 
 This archive contains the distribution LIMS2-WebApp,
-version 0.052:
+version 0.054:
 
   Catalyst based application
 

diff --git a/lib/LIMS2/AlleleRequest.pm b/lib/LIMS2/AlleleRequest.pm
@@ -1,7 +1,7 @@
 package LIMS2::AlleleRequest;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::AlleleRequest::VERSION = '0.052';
+    $LIMS2::AlleleRequest::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/AlleleRequest/DoubleTargeted.pm b/lib/LIMS2/AlleleRequest/DoubleTargeted.pm
@@ -1,7 +1,7 @@
 package LIMS2::AlleleRequest::DoubleTargeted;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::AlleleRequest::DoubleTargeted::VERSION = '0.052';
+    $LIMS2::AlleleRequest::DoubleTargeted::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/AlleleRequest/SingleTargeted.pm b/lib/LIMS2/AlleleRequest/SingleTargeted.pm
@@ -1,7 +1,7 @@
 package LIMS2::AlleleRequest::SingleTargeted;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::AlleleRequest::SingleTargeted::VERSION = '0.052';
+    $LIMS2::AlleleRequest::SingleTargeted::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/AlleleRequestFactory.pm b/lib/LIMS2/AlleleRequestFactory.pm
@@ -1,7 +1,7 @@
 package LIMS2::AlleleRequestFactory;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::AlleleRequestFactory::VERSION = '0.052';
+    $LIMS2::AlleleRequestFactory::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/CassetteFunction.pm b/lib/LIMS2/CassetteFunction.pm
@@ -1,7 +1,7 @@
 package LIMS2::CassetteFunction;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::CassetteFunction::VERSION = '0.052';
+    $LIMS2::CassetteFunction::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Catalyst/Controller/REST.pm b/lib/LIMS2/Catalyst/Controller/REST.pm
@@ -1,7 +1,7 @@
 package LIMS2::Catalyst::Controller::REST;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Catalyst::Controller::REST::VERSION = '0.052';
+    $LIMS2::Catalyst::Controller::REST::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model.pm b/lib/LIMS2/Model.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::VERSION = '0.052';
+    $LIMS2::Model::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model/AuthDB.pm b/lib/LIMS2/Model/AuthDB.pm
@@ -3,7 +3,7 @@ use utf8;
 package LIMS2::Model::AuthDB;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::AuthDB::VERSION = '0.052';
+    $LIMS2::Model::AuthDB::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model/Constants.pm b/lib/LIMS2/Model/Constants.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::Constants;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::Constants::VERSION = '0.052';
+    $LIMS2::Model::Constants::VERSION = '0.054';
 }
 ## use critic
 
@@ -32,6 +32,7 @@ const our %PROCESS_PLATE_TYPES => (
     cre_bac_recom          => [qw( INT )],
     '2w_gateway'           => [qw( POSTINT FINAL )],
     '3w_gateway'           => [qw( POSTINT FINAL )],
+    final_pick             => [qw( FINAL_PICK )],
     dna_prep               => [qw( DNA )],
     recombinase            => [qw( FINAL XEP POSTINT )],
     first_electroporation  => [qw( EP )],
@@ -55,6 +56,7 @@ const our %PROCESS_TEMPLATE => (
     cre_bac_recom          => 'recombineering_template.csv',
     '2w_gateway'           => 'gateway_template.csv',
     '3w_gateway'           => 'gateway_template.csv',
+    final_pick             => 'standard_template.csv',
     dna_prep               => 'standard_template.csv',
     recombinase            => 'recombinase_template.csv',
     first_electroporation  => 'first_electroporation_template.csv',
@@ -64,6 +66,8 @@ const our %PROCESS_TEMPLATE => (
     freeze                 => 'standard_template.csv',
 );
 
+# number relates to number of input wells (e.g. an SEP has two inputs)
+# and type to their plate type(s). N.B. if you don't specify a type then any is fine
 const our %PROCESS_INPUT_WELL_CHECK => (
     create_di => { number => 0 },
     int_recom => {
@@ -78,14 +82,18 @@ const our %PROCESS_INPUT_WELL_CHECK => (
         type   => [qw( INT )],
         number => 1,
     },
+    final_pick => {
+        type   => [qw( FINAL FINAL_PICK )],
+        number => 1,
+    },
     recombinase   => { number => 1 },
     cre_bac_recom => {
         type   => [qw( DESIGN )],
         number => 1,
     },
     rearray  => { number => 1 },
     dna_prep => {
-        type   => [qw( FINAL )],
+        type   => [qw( FINAL FINAL_PICK )],
         number => 1,
     },
     clone_pick => {

diff --git a/lib/LIMS2/Model/DBConnect.pm b/lib/LIMS2/Model/DBConnect.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::DBConnect;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::DBConnect::VERSION = '0.052';
+    $LIMS2::Model::DBConnect::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model/FormValidator.pm b/lib/LIMS2/Model/FormValidator.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::FormValidator;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::FormValidator::VERSION = '0.052';
+    $LIMS2::Model::FormValidator::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model/FormValidator/Constraint.pm b/lib/LIMS2/Model/FormValidator/Constraint.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::FormValidator::Constraint;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::FormValidator::Constraint::VERSION = '0.052';
+    $LIMS2::Model::FormValidator::Constraint::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model/Plugin/BAC.pm b/lib/LIMS2/Model/Plugin/BAC.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::Plugin::BAC;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::Plugin::BAC::VERSION = '0.052';
+    $LIMS2::Model::Plugin::BAC::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model/Plugin/Design.pm b/lib/LIMS2/Model/Plugin/Design.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::Plugin::Design;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::Plugin::Design::VERSION = '0.052';
+    $LIMS2::Model::Plugin::Design::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model/Plugin/Gene.pm b/lib/LIMS2/Model/Plugin/Gene.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::Plugin::Gene;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::Plugin::Gene::VERSION = '0.052';
+    $LIMS2::Model::Plugin::Gene::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model/Plugin/GenotypingQC.pm b/lib/LIMS2/Model/Plugin/GenotypingQC.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::Plugin::GenotypingQC;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::Plugin::GenotypingQC::VERSION = '0.052';
+    $LIMS2::Model::Plugin::GenotypingQC::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model/Plugin/Plate.pm b/lib/LIMS2/Model/Plugin/Plate.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::Plugin::Plate;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::Plugin::Plate::VERSION = '0.052';
+    $LIMS2::Model::Plugin::Plate::VERSION = '0.054';
 }
 ## use critic
 
@@ -200,6 +200,7 @@ sub set_plate_assay_complete {
     my $validated_params = $self->check_params( $params, $self->pspec_set_plate_assay_complete,
         ignore_unknown => 1 );
 
+
     my $plate = $self->retrieve_plate($params);
 
     for my $well ( $plate->wells ) {
@@ -213,6 +214,84 @@ sub set_plate_assay_complete {
     return $plate;
 }
 
+=head
+Method: create_plate_by_copy
+
+Takes an input plate (that must exist), and creates a copy of the plate ready for well
+data to be imported by csv upload.
+=cut
+
+
+sub pspec_create_plate_by_copy {
+    return {
+        from_plate_name  =>      { validate => 'plate_name' },
+        to_plate_name    =>      { validate => 'plate_name' },
+        created_by       =>      { validate => 'existing_user' },
+        created_at       =>      { validate => 'date_time', optional => 1, post_filter => 'parse_date_time' },
+
+    };
+}
+
+sub create_plate_by_copy {
+    my ( $self, $params ) = @_;
+    my $validated_params = $self->check_params( $params, $self->pspec_create_plate_by_copy );
+    my $from_plate_name = $validated_params->{'from_plate_name'};
+    my $to_plate_name = $validated_params->{'to_plate_name'};
+    my $this_user = $validated_params->{'created_by'};
+
+    my $from_plate
+        = $self->schema->resultset('Plate')->find( { name => $from_plate_name } );
+    if (! $from_plate) {
+        $self->throw( Validation => 'Plate ' . $from_plate_name . ' does not exist' );
+    }
+
+    my $to_plate
+        = $self->schema->resultset('Plate')->find( { name => $to_plate_name } );
+    if ( $to_plate ) {
+        $self->throw( Validation => 'Plate ' . $to_plate_name . ' already exists' );
+    }
+#
+# Get the wells from the plate we need to copy
+#
+#
+    my $well_rs = $self->schema->resultset( 'Well' );
+
+    my @wells_on_plate = $well_rs->search( { 'plate.name' => $from_plate_name },
+        {
+            join => [ 'plate' ],
+        }
+    );
+
+# process the well data into @well_data
+    my $process_type = 'dna_prep';
+    my @well_data = ();
+
+    foreach my $well ( @wells_on_plate ) {
+        my %well_hash;
+        $well_hash{'well_name'} = $well->name;
+        $well_hash{'parent_plate'} = $from_plate->name;
+        $well_hash{'parent_well'} = $well->name;
+        $well_hash{'process_type'} = $process_type;
+        push @well_data, \%well_hash;
+    }
+
+
+    my $plate = $self->create_plate(
+        {
+            name =>  $to_plate_name ,
+            description => $from_plate->description,
+            type => 'DNA',
+            created_by => $this_user,
+            species => $from_plate->species->id,
+            wells => \@well_data,
+        }
+    );
+    $plate->discard_changes;
+
+    return $plate;
+}
+
+
 sub create_plate_csv_upload {
     my ( $self, $params, $well_data_fh ) = @_;
 

diff --git a/lib/LIMS2/Model/Plugin/Process.pm b/lib/LIMS2/Model/Plugin/Process.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::Plugin::Process;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::Plugin::Process::VERSION = '0.052';
+    $LIMS2::Model::Plugin::Process::VERSION = '0.054';
 }
 ## use critic
 

diff --git a/lib/LIMS2/Model/Plugin/ProcessTree.pm b/lib/LIMS2/Model/Plugin/ProcessTree.pm
@@ -1,7 +1,7 @@
 package LIMS2::Model::Plugin::ProcessTree;
 ## no critic(RequireUseStrict,RequireUseWarnings)
 {
-    $LIMS2::Model::Plugin::ProcessTree::VERSION = '0.052';
+    $LIMS2::Model::Plugin::ProcessTree::VERSION = '0.054';
 }
 ## use critic