Merge branch 'devel' into report_cacheing

htgt · Jul 30, 2012 · 4f64699 · 4f64699
2 parents a3b9539 + 29ba220
commit 4f64699
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diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,4 @@ ddl/lims2_test
 ddl/lims2_test2
 ddl/lims2_live
 ddl/lims2_staging
+ddl/lims2_sp12
diff --git a/Changes b/Changes
@@ -1,6 +1,9 @@
 {{$NEXT}}
 
+0.011     2012-07-26 16:06:14 Europe/London
+
    Implement electroporation detail and summary reports.
+   Bugfix mouse gene retrieval; resolves #8713.
 
 0.010     2012-07-25 13:08:51 Europe/London
 

diff --git a/ddl/templates/versions/7/fixtures.sql b/ddl/templates/versions/7/fixtures.sql
@@ -34,3 +34,5 @@ VALUES ('blue_colonies'),
        ('picked_colonies'),
        ('total_colonies'),
        ('remaining_unstained_colonies'); 
+
+INSERT INTO schema_versions(version) VALUES (7);
diff --git a/lib/LIMS2/Model/Plugin/Gene.pm b/lib/LIMS2/Model/Plugin/Gene.pm
@@ -113,15 +113,15 @@ sub _retrieve_solr_gene {
         $genes = $self->solr_query( [ ensembl_gene_id => $search_term ] );
     }
     else {
-        $genes = $self->solr_query( [ marker_symbol => $search_term ] );
+        $genes = $self->solr_query( [ marker_symbol_str => $search_term ] );
     }
 
     if ( @{$genes} == 0 ) {
         $self->throw( NotFound => { entity_class => 'Gene', search_params => $params } );
     }
 
     if ( @{$genes} > 1 ) {
-        $self->throw( Implemnetation => "Retrieval of gene Mouse/$search_term returned " . @{$genes} . " genes" );
+        $self->throw( Implementation => "Retrieval of gene Mouse/$search_term returned " . @{$genes} . " genes" );
     }
 
     return $self->_normalize_solr_result( shift @{$genes} );

diff --git a/t/50-model-plugin-design.t b/t/50-model-plugin-design.t
@@ -7,7 +7,7 @@ use LIMS2::Test;
 use Test::Most;
 
 {
-    ok my $design = model->retrieve_design( { id => 95 } ), 'retrieve design id=95';
+    ok my $design = model->retrieve_design( { id => 84231 } ), 'retrieve design id=84231';
     isa_ok $design, 'LIMS2::Model::Schema::Result::Design';
     can_ok $design, 'as_hash';
     ok my $h1 = $design->as_hash(), 'as hash, with relations';
@@ -18,14 +18,14 @@ use Test::Most;
 }
 
 {
-    ok my $designs = model->list_assigned_designs_for_gene( { species => 'Mouse', gene_id => 'MGI:1915248' } ), 'list assigned designs by MGI accession';
+    ok my $designs = model->list_assigned_designs_for_gene( { species => 'Mouse', gene_id => 'MGI:94912' } ), 'list assigned designs by MGI accession';
     isa_ok $designs, ref [];
     ok @{$designs} > 0, '...the list is not empty';
     isa_ok $_, 'LIMS2::Model::Schema::Result::Design' for @{$designs};    
 }
 
 {
-    ok my $designs = model->list_assigned_designs_for_gene( { species => 'Mouse', gene_id => 'MGI:1915248', type => 'conditional' } ),
+    ok my $designs = model->list_assigned_designs_for_gene( { species => 'Mouse', gene_id => 'MGI:106032', type => 'conditional' } ),
         'list assigned designs by MGI accession and design type conditional';
     isa_ok $designs, ref [];
     ok @{$designs} > 0, '...the list is not empty';
@@ -39,10 +39,10 @@ use Test::Most;
 }
 
 {
-    ok my $designs = model->list_candidate_designs_for_gene( { species => 'Mouse', gene_id => 'MGI:1915248' } ),
+    ok my $designs = model->list_candidate_designs_for_gene( { species => 'Mouse', gene_id => 'MGI:94912' } ),
         'list candidate designs for MGI accession';
     isa_ok $designs, ref [];
-    ok grep( { $_->id == 95 } @{$designs} ), '...returns the expected design';
+    ok grep( { $_->id == 170606 } @{$designs} ), '...returns the expected design';
 }
 
 done_testing;
diff --git a/t/50-model-plugin-plate.t b/t/50-model-plugin-plate.t
@@ -40,7 +40,7 @@ note( "Testing plate retrieve" );
     ok my $plate = model->retrieve_plate( $plate_data->{plate_retrieve} ),
         'retrieve_plate by name should succeed';
     isa_ok $plate, 'LIMS2::Model::Schema::Result::Plate';
-    is $plate->name, 'PCS100', 'retrieved correct plate';
+    is $plate->name, 'PCS00075_A', 'retrieved correct plate';
 }
 
 done_testing();
diff --git a/t/50-model-plugin-process.t b/t/50-model-plugin-process.t
@@ -24,16 +24,16 @@ my $create_di_process_data= test_data( 'create_di_process.yaml' );
         'process is of correct type';
 
     ok my $process_design = $process->process_design, 'process has a process_design';
-    is $process_design->design_id, 1, 'process_design has correct design_id';
+    is $process_design->design_id, 95120, 'process_design has correct design_id';
     ok my $process_bacs = $process->process_bacs, 'process has process_bacs';
     is $process_bacs->count, 1, 'only has one bac';
     ok my $bac_clone = $process_bacs->next->bac_clone, 'can retrieve bac clone from process';
-    is $bac_clone->name, 'CT7-156D8', '.. and has correct bac_clone';
+    is $bac_clone->name, 'RP24-135L5', '.. and has correct bac_clone';
 
     ok my $output_wells = $process->output_wells, 'process can return output wells resultset';
     is $output_wells->count, 1, 'only one output well';
     my $output_well = $output_wells->next;
-    is $output_well->name, 'A01', 'output well has correct name';
+    is $output_well->name, 'F06', 'output well has correct name';
     is $output_well->plate->name, '100', '..and is on correct plate';
 }
 
@@ -64,14 +64,14 @@ my $int_recom_process_data= test_data( 'int_recom_process.yaml' );
     ok my $input_wells = $process->input_wells, 'process can return input wells resultset';
     is $input_wells->count, 1, 'only one input well';
     my $input_well = $input_wells->next;
-    is $input_well->name, 'A01', 'input well has correct name';
+    is $input_well->name, 'F06', 'input well has correct name';
     is $input_well->plate->name, '100', '..and is on correct plate';
 
     ok my $output_wells = $process->output_wells, 'process can return output wells resultset';
     is $output_wells->count, 1, 'only one output well';
     my $output_well = $output_wells->next;
-    is $output_well->name, 'A01', 'output well has correct name';
+    is $output_well->name, 'G02', 'output well has correct name';
-    is $output_well->plate->name, 'PCS100', '..and is on correct plate';
+    is $output_well->plate->name, 'PCS00177_A', '..and is on correct plate';
 }
 
 throws_ok {
@@ -80,7 +80,7 @@ throws_ok {
 
 throws_ok {
     my $process = model->create_process( $int_recom_process_data->{invalid_input_well} );
-} qr/int_recom process input well should be type DESIGN \(got POSTINT\)/;
+} qr/int_recom process input well should be type DESIGN \(got EP\)/;
 
 
 note( "Testing 2w_gateway process creation" );
@@ -99,14 +99,14 @@ my $process_data_2w_gateway= test_data( '2w_gateway_process.yaml' );
     ok my $input_wells = $process->input_wells, 'process can return input wells resultset';
     is $input_wells->count, 1, 'only one input well';
     my $input_well = $input_wells->next;
-    is $input_well->name, 'A01', 'input well has correct name';
+    is $input_well->name, 'G02', 'input well has correct name';
-    is $input_well->plate->name, 'PCS100', '..and is on correct plate';
+    is $input_well->plate->name, 'PCS00177_A', '..and is on correct plate';
 
     ok my $output_wells = $process->output_wells, 'process can return output wells resultset';
     is $output_wells->count, 1, 'only one output well';
     my $output_well = $output_wells->next;
     is $output_well->name, 'A01', 'output well has correct name';
-    is $output_well->plate->name, 'PGS100', '..and is on correct plate';
+    is $output_well->plate->name, 'MOHSAS0001_A', '..and is on correct plate';
 
     ok my $process_recombinases = $process->process_recombinases, 'process has process_recombinases';
     is $process_recombinases->count, 1, 'has 1 recombinase';
@@ -144,14 +144,14 @@ my $process_data_3w_gateway= test_data( '3w_gateway_process.yaml' );
     ok my $input_wells = $process->input_wells, 'process can return input wells resultset';
     is $input_wells->count, 1, 'only one input well';
     my $input_well = $input_wells->next;
-    is $input_well->name, 'A01', 'input well has correct name';
+    is $input_well->name, 'G02', 'input well has correct name';
-    is $input_well->plate->name, 'PCS100', '..and is on correct plate';
+    is $input_well->plate->name, 'PCS00177_A', '..and is on correct plate';
 
     ok my $output_wells = $process->output_wells, 'process can return output wells resultset';
     is $output_wells->count, 1, 'only one output well';
     my $output_well = $output_wells->next;
     is $output_well->name, 'A01', 'output well has correct name';
-    is $output_well->plate->name, 'PGS100', '..and is on correct plate';
+    is $output_well->plate->name, 'MOHSAS0001_A', '..and is on correct plate';
 
     ok my $process_recombinases = $process->process_recombinases, 'process has process_recombinases';
     is $process_recombinases->count, 1, 'has 1 recombinase';
@@ -184,14 +184,14 @@ my $cre_bac_recom_process_data= test_data( 'cre_bac_recom_process.yaml' );
     ok my $input_wells = $process->input_wells, 'process can return input wells resultset';
     is $input_wells->count, 1, 'only one input well';
     my $input_well = $input_wells->next;
-    is $input_well->name, 'A01', 'input well has correct name';
+    is $input_well->name, 'F06', 'input well has correct name';
     is $input_well->plate->name, '100', '..and is on correct plate';
 
     ok my $output_wells = $process->output_wells, 'process can return output wells resultset';
     is $output_wells->count, 1, 'only one output well';
     my $output_well = $output_wells->next;
     is $output_well->name, 'A01', 'output well has correct name';
-    is $output_well->plate->name, 'PCS100', '..and is on correct plate';
+    is $output_well->plate->name, 'MOHSAS0001_A', '..and is on correct plate';
 }
 
 throws_ok {
@@ -211,14 +211,14 @@ my $recombinase_process_data= test_data( 'recombinase_process.yaml' );
     ok my $input_wells = $process->input_wells, 'process can return input wells resultset';
     is $input_wells->count, 1, 'only one input well';
     my $input_well = $input_wells->next;
-    is $input_well->name, 'A01', 'input well has correct name';
+    is $input_well->name, 'G02', 'input well has correct name';
-    is $input_well->plate->name, 'PCS100', '..and is on correct plate';
+    is $input_well->plate->name, 'PCS00177_A', '..and is on correct plate';
 
     ok my $output_wells = $process->output_wells, 'process can return output wells resultset';
     is $output_wells->count, 1, 'only one output well';
     my $output_well = $output_wells->next;
     is $output_well->name, 'A01', 'output well has correct name';
-    is $output_well->plate->name, 'PGS100', '..and is on correct plate';
+    is $output_well->plate->name, 'MOHSAS0001_A', '..and is on correct plate';
 
     ok my $process_recombinases = $process->process_recombinases, 'process has process_recombinases';
     is $process_recombinases->count, 1, 'has 1 recombinase';
@@ -239,13 +239,13 @@ my $rearray_process_data= test_data( 'rearray_process.yaml' );
     is $input_wells->count, 1, 'only one input well';
     my $input_well = $input_wells->next;
     is $input_well->name, 'A01', 'input well has correct name';
-    is $input_well->plate->name, 'PCS100', '..and is on correct plate';
+    is $input_well->plate->name, 'MOHFAS0001_A', '..and is on correct plate';
 
     ok my $output_wells = $process->output_wells, 'process can return output wells resultset';
     is $output_wells->count, 1, 'only one output well';
     my $output_well = $output_wells->next;
     is $output_well->name, 'A01', 'output well has correct name';
-    is $output_well->plate->name, 'PCS200', '..and is on correct plate';
+    is $output_well->plate->name, 'MOHSAS0001_A', '..and is on correct plate';
 }
 
 throws_ok {
@@ -266,13 +266,13 @@ my $dna_prep_process_data= test_data( 'dna_prep_process.yaml' );
     is $input_wells->count, 1, 'only one input well';
     my $input_well = $input_wells->next;
     is $input_well->name, 'A01', 'input well has correct name';
-    is $input_well->plate->name, 'FINAL100', '..and is on correct plate';
+    is $input_well->plate->name, 'MOHSAS0001_A', '..and is on correct plate';
 
     ok my $output_wells = $process->output_wells, 'process can return output wells resultset';
     is $output_wells->count, 1, 'only one output well';
     my $output_well = $output_wells->next;
     is $output_well->name, 'A01', 'output well has correct name';
-    is $output_well->plate->name, 'PGS100', '..and is on correct plate';
+    is $output_well->plate->name, 'MOHSAQ0001_A_2', '..and is on correct plate';
 }
 
 throws_ok {

diff --git a/t/50-model-plugin-well.t b/t/50-model-plugin-well.t
@@ -21,8 +21,8 @@ note( "Testing well creation" );
         'create_well should succeed';
     isa_ok $well, 'LIMS2::Model::Schema::Result::Well';
     is $well->created_by->name, 'test_user@example.org', 'well has correct created by user';
-    is $well->name, 'B01', 'well has correct name';
+    is $well->name, 'A01', 'well has correct name';
-    is $well->plate->name, 'PCS100', 'well belongs to correct plate';
+    is $well->plate->name, 'PCS00177_A', 'well belongs to correct plate';
 
     ok my $retrieve_well = model->retrieve_well( { id => $well->id } ),
         'retrieve_well by id should succeed';
@@ -35,7 +35,7 @@ note( "Testing well creation" );
         'retrieve_plate by name should succeed';
     isa_ok $well, 'LIMS2::Model::Schema::Result::Well';
     is $well->name, 'A01', 'retrieved correct well';
-    is $well->plate->name, 'PCS100', '.. on correct plate';
+    is $well->plate->name, 'PCS00177_A', '.. on correct plate';
 
     note( "Testing create well accepted override" );
     ok my $override = model->create_well_accepted_override( $well_data->{well_accepted_override_create} ),
@@ -102,7 +102,7 @@ note( "Testing well creation" );
     note( "Testing delete_well" );
 
     lives_ok {
-        model->delete_well( { plate_name => 'PCS100', well_name => 'B01' } )
+        model->delete_well( { plate_name => 'PCS00177_A', well_name => 'A01' } )
     } 'delete well';
 }
 

diff --git a/t/data/2w_gateway_process.yaml b/t/data/2w_gateway_process.yaml
@@ -3,33 +3,33 @@ valid_input:
     type: 2w_gateway
     cassette: L1L2_Bact_P
     output_wells:
-        - plate_name: PGS100
+        - plate_name: MOHSAS0001_A
           well_name: A01
     input_wells: 
-        - plate_name: PCS100
+        - plate_name: PCS00177_A
-          well_name: A01
+          well_name: G02
     recombinase:
         - Cre
 require_cassette_or_backbone:
     type: 2w_gateway
     output_wells:
-        - plate_name: PGS100
+        - plate_name: MOHSAS0001_A
           well_name: A01
     input_wells: 
-        - plate_name: PCS100
+        - plate_name: PCS00177_A
-          well_name: A01
+          well_name: G02
 missing_input_well:
     type: 2w_gateway
     cassette: L1L2_Bact_P
     output_wells:
-        - plate_name: PCS100
+        - plate_name: MOHSAS0001_A
           well_name: A01
 invalid_input_well:
     type: 2w_gateway
     cassette: L1L2_Bact_P
     output_wells:
-        - plate_name: PCS100
+        - plate_name: MOHSAS0001_A
           well_name: A01
     input_wells: 
         - plate_name: 100
-          well_name: A01
+          well_name: F06
diff --git a/t/data/3w_gateway_process.yaml b/t/data/3w_gateway_process.yaml
@@ -4,27 +4,27 @@ valid_input:
     cassette: L1L2_Bact_P
     backbone: L3L4_pZero_kan
     output_wells:
-        - plate_name: PGS100
+        - plate_name: MOHSAS0001_A
           well_name: A01
     input_wells: 
-        - plate_name: PCS100
+        - plate_name: PCS00177_A
-          well_name: A01
+          well_name: G02
     recombinase:
         - Cre
 missing_input_well:
     type: 3w_gateway
     cassette: L1L2_Bact_P
     backbone: L3L4_pZero_kan
     output_wells:
-        - plate_name: PCS100
+        - plate_name: MOHSAS0001_A
           well_name: A01
 invalid_input_well:
     type: 3w_gateway
     cassette: L1L2_Bact_P
     backbone: L3L4_pZero_kan
     output_wells:
-        - plate_name: PCS100
+        - plate_name: MOHSAS0001_A
           well_name: A01
     input_wells: 
         - plate_name: 100
-          well_name: A01
+          well_name: F06
diff --git a/t/data/cre_bac_recom_process.yaml b/t/data/cre_bac_recom_process.yaml
@@ -2,20 +2,20 @@
 valid_input:
     type: cre_bac_recom
     output_wells:
-        - plate_name: PCS100
+        - plate_name: MOHSAS0001_A
           well_name: A01
     input_wells: 
         - plate_name: 100
-          well_name: A01
+          well_name: F06
     cassette: pR6K_R1R2_ZP
     backbone: R3R4_pBR_amp
 invalid_input_well:
     type: cre_bac_recom
     output_wells:
-        - plate_name: PGS100
+        - plate_name: MOHSAS0001_A
           well_name: A01
     input_wells:
-        - plate_name: PCS100
+        - plate_name: PCS00177_A
-          well_name: A01
+          well_name: G02
     cassette: pR6K_R1R2_ZP
     backbone: R3R4_pBR_amp